The gates of hell won't prevail against the church (Matt 16:18), but the beast is given authority to conquer the saints (Rev 13:7)

"[the Beast] was allowed to make war on the saints and to conquer them [but] the gates of hell shall not prevail against [the church]" sounds fine to me.

We know from Daniel 7, Revelation, Isaiah and other places Jesus returns to conquer and deliver before "And except those days should be shortened, there should no flesh be saved" (Matthew 24:22)

First, the Dispensationalist explanation you allude to is not reasonable, given that there is not even a hint of a secret ‘rapture’ of the Church prior to Revelation’s ‘great tribulation’ period. It is also not reasonable due to the fact that there are only ever two presences of Christ – his first one when he came in the flesh as Mary’s child, then his spectacular return when he comes to suddenly start the day of resurrection and judgment, when time is no more. It is only at that point that the Bible speaks of the saints (those who belong to Christ by faith) who are alive on earth at that time being caught up to join Christ in the air, following hard on the heels of the resurrected bodies of saints who arise first. However, there IS a reasonable, non-dispensationalist interpretation which is so startling, it calls for a re-think of what Jesus meant when he promised that the gates of hell / hades would never overcome his Church.

As I am on holiday and the text from a qualified theologian from which I would have quoted is neither on-line nor stored on my laptop, I can only call upon my memory.

These particular gates are usually viewed as prevailing against the gathered Church by defeating and destroying the Church. The general idea most people seem to have is of those symbolic gates opening to let out hordes of enemies of the Church in order to destroy it – knocking it off the Rock it is built upon, casting it into a ruinous heap, as if it were a religious institution built on sand, not rock. Although there was, indeed, serious persecution of the Church (the saints on earth) towards the end of the first century A.D. and into the second, history shows that such vicious attacks have been happening on and off for nearly 2,000 years now, with the present century seeing the most massive and concerted attacks ever against Christians the world over.

But here is the gist of one Baptist minister’s points about Matthew 16:18, and what those ‘gates of hell/hades’ signify. He starts by showing that gates are primarily designed to keep things in: the stable gate is bolted before the horse escapes, so that it cannot escape: prison gates are locked and barred to keep all the prisoners in. Hell and hades not only want to keep all their prisoners, they want to drag in far more poor souls, for eternity. Only the Church that Christ builds thwarts such devilish work, which is why all kinds of evil devices are employed by Satan’s minions to attack Christ’s Church, which is the only force in all creation equipped by Christ to overcome sin, death and hell, because he has first liberated its members in order to make them members of his triumphant Church. The gates of hell/hades are powerless to keep inside its domain those whom Christ has elected unto salvation. They find themselves released, liberated from being behind those gates, for they now stand in the glorious freedom of Christ, part of his earthly Church. And of such ones Christ promises that the gates of hell/hades will never prevail against them, because HE has prevailed, and none can undo what he has accomplished.

Sadly, there remains the tragedy of those who are imprisoned in spiritual darkness which is all that they have ever known, being born into it, but they cannot, by their own efforts, effect release; their captors will not open the gates of hell/hades to let them out; they cannot scale its monumental, barbed walls; they cannot dig down, under and beyond its dank foundations. Nothing but a miracle from above can lift them out. Oh, many have hope that because they are able to march around the internal exercise yard that that will effect release – they look up to a heavenly blue sky above and suppose they might get whisked up and away [pre-trib rapture believers?]. Has it not dawned on them that if they already belonged to Christ by faith, they would never be in the grips of a satanic system? Yet all religious systems that commit spiritual adultery with the world are hell-bound.

As they walk around the yard, talking with others of like mind, they pray and sing, and listen to leaders who tell them that they can witness to other prisoners and guards, and thus the Church of Christ will grow, right there. They can rejoice that the Church is at work and that the gates of hell/hades have not prevailed against them – they do not even see that they are locked within its domain! But they are in the world, and this world is in the grips of Satan and his deceptions. They seem to be content to be in the world, enjoying its benefits, while thinking they can still be Christians, witnessing to others. Of course, they are not content to be persecuted but (strangely), professing believers who keep doing the desires of this world just don’t seem to be persecuted much at all. Why not? Because they are already locked in behind the gates of hell/hades and not yet liberated into the glorious freedom of the children of God. No amount of marching round the exercise yard will cause the gates of hell/hades to open up to them! [Rev. Guy R. Finnie, Portsmouth Baptist Church magazine, circa 1990.]

In that sense, the gates of hell/hades have already prevailed against those who merely suppose that they must be Christians because they were born into that religion, or converted to following a system that claims to enable them to eventually get saved. But Jesus never promised those ones to be free from such deceptive bondage. He only made the promise to those, who like Peter, had a revelation from God as to just who Jesus Christ really is, leading to confess him alone as their Saviour and Lord (Mat. 16:15-17). Those – in every century - comprise ‘the Church’ that can never be prevailed against. Now, after seeing Mat. 16:18 in that light, what about Rev. 13:7?

Let me switch to another Protestant believer who has written the following:

“Chapter 13 reveals the two global concepts – depicted as powers or authorities – by which that adversary [Satan] deceives the whole world, and challenges Christ lawfully to recover the throne and dominion which he himself had usurped by spiritual wickedness. The powers, authorities, or means by which this wickedness is established and sustained are depicted as two beasts. This is the allegory… ‘I am he that liveth, and was dead; and behold. I am alive forevermore, Amen; and have the keys of hell and of death’, Chapter 1:18. Here, Christ’s having the keys of hell and of death follow immediately – and consequently – upon his being raised from the dead to live forevermore, Amen. Then, the keys were obtained lawfully through his death, when the hour of the prince of darkness was come, the curse of the law fell upon the Redeemer, and, through death, he not only delivered his people from the curse, but in himself took them through death, beyond the grave, and therefore for ever out of the reach of the law. Thus he led captivity captive, spoiled principalities and powers, and made a show of them openly. Through death he destroyed – the Greek means, To make of none effect – him that had the power of death, that is, the devil, and delivered them who – under the law – through fear of death were all their lifetime subject to bondage, Hebrews 2:14,15.” [The Revelation of Jesus Christ, John Metcalfe, pages 304 & 541-542, published 1998.]

That was when Christ prevailed against the gates of hell and death, unlocking its gates to release all of his choosing who were locked behind them in every age. From that moment on, the gates of hell could never prevail against those whom Christ liberated and will yet liberate. Not even when God allows those two beastly agents of Satan to war against the saints on earth does Satan prevail against the Church. The ungodly think those saints have been overcome because they only see with their eyes, and do not understand spiritual verities. They have been deceived and have no idea that Christ prevailed against the gates of hell/hades due to his crucifixion. Consider the account in Mat. 27:50-54 about the dead saints arising from their graves at that very moment! From there-on Christ unlocks those gates to let out whosoever he will. The ungodly see none of this, for they are blindly following the deceptions of Satan even while they remain locked within his worldly empire.

Those who belong to Christ’s Church are given revelation to see how the gates of hell cannot ever prevail against her, for their Lord has the keys of death and hell. Despite physical persecutions and martyrs of the saints on earth, right up until his second coming (not a third one) the Church remains triumphant and, when it is too late for anyone to flee Babylon the spiritual fornicator or Babylon the great city, those deceived by Satan will wail at seeing Christ return in glory – Rev. 1:7.

How would someone who doesn't believe in a pre-tribulation rapture harmonize the following two verses?

Many Christian nations have been (literally) conquered by expanding non-Christian religions, but this is not seen as contradicting Matthew's account, since that passage is not usually interpreted (by anyone, regardless of denomination) as meaning or implying that there will be no martyrdom or anti-Christian persecution, which is what the Revelation of John is mainly about.

The only way in which the two quotes could possibly be at odds with one another is if one were to interpret the former in the traditional (pre-Protestant) sense, and the latter as referring to the physical annihilation of all Christendom (because otherwise, countless Christians have been enslaved, oppressed, persecuted, or killed in large amounts by non-Christians throughout history, but no one sees this as infringing on Matthew's Gospel), followed by business as usual (as opposed to the end of the world, which is what the Book of Revelation is [also] about).

This answer addresses the question from a Catholic perspective. I do not presume to speak for any other denominations.

The Catholic interpretation of the book of Revelation places it in a larger tradition of "apocalypses": works that encourage resistance to an oppressor, using heavily symbolic and coded language that a contemporary audience would understand, but which is harder to decipher today. Modern Christians can certainly draw value from it, but it was not written with us in mind.

The Book of Revelation was written for people who were living during the time of the author. Other apocalyptic books, like the Book of Revelation, are in the Old Testament: Daniel, parts of Ezekiel, Judith, and others. It is this type of writing, as Fr. Doyle shows, that is full of symbolism and uses codes words or names to hide the real message from the persecutors of those who would understand what the author is writing about. This type of writing was meant to encourage those enduring persecution. If the persecutors came across this subversive writing they would not know what it was saying or would think it was something from the past. This was a protection method for those who understood the writing’s symbolism and codes.

—Catholic News Agency

The Book of Revelation cannot be adequately understood except against the historical background that occasioned its writing. Like Daniel and other apocalypses, it was composed as resistance literature to meet a crisis. The book itself suggests that the crisis was ruthless persecution of the early church by the Roman authorities; the harlot Babylon symbolizes pagan Rome, the city on seven hills (Rev 17:9). The book is, then, an exhortation and admonition to Christians of the first century to stand firm in the faith and to avoid compromise with paganism, despite the threat of adversity and martyrdom; they are to await patiently the fulfillment of God’s mighty promises.

—United States Conference of Catholic Bishops

Looking more specifically at the (first) Beast, the general consensus is that it represents the historical Roman Empire as led by Emperor Nero.

What Daniel’s four beasts have in common is that they are all pagan kingdoms that persecuted and conquered God’s people, Israel. John’s beast [which shares aspects of all four] is the same kind of thing—a conquering pagan empire. Since it comes after Daniel’s four beasts, Rome is the logical candidate. But it’s not a future, “restored Roman Empire.” It’s the real thing, the pagan Roman Empire of the early centuries. This is confirmed by several lines of evidence.

First, the book of Revelation is explicit in stating that it concerns events that will happen “soon” (1:1, 2:16, 3:11, 22:6, 7, 12, 20). This indicates that the bulk of the events of the book (those that precede the Millennium of Rev. 20:1-10, in which we are now living) should take place shortly after the book was written, likely in the A.D. 60s.

Second, we are told that the number of the beast is 666 and that this is the number of a man’s name (13:18). Not coincidentally, the persecuting, pagan Roman Empire was headed in the A.D. 60s by Caesar Nero, whose name happened to add up to 666 in the Hebrew system of letters and numbers. (In Hebrew, “Caesar Nero” = “NRWN QSR” = N 50 + R 200 + W 6 + N 50 + Q 100 + S 60 + R 200 = 666; a variant spelling of the name, NRW QSR, adds up to 616, which some manuscripts have in place of 666).

Third, the seven heads of the beast are identified as seven mountains (17:9). Though this is not certain, these are likely the seven hills on which the city of Rome was built. (Vatican Hill, however, was not one of the seven; it is on the side of the Tiber River opposite the seven.)

Thus there is good evidence that the beast from the sea is the pagan Roman Empire of the first century and, in particular, the emperor at its head. This, again, is like Daniel’s four beasts, who were described both as four kings (Dan 7:17) and four kingdoms (cf. Dan. 7:23).

—Catholic Answers

In this context, "[the Beast]...mak[ing] war on the saints" would refer to the historical events of Nero's persecutions against the early Christians. Therefore there is no conflict with Matthew 16:18. The church is still here, and Nero is not.