What are the most common reasons that cause Christians to deconvert to atheism/agnosticism?

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What's wrong?

What are the most common reasons that cause Christians to lose their faith and turn to atheism, agnosticism or skepticism?

Well... it's hard to arrive at a factual answer. The only thing I found without spending hours doing research was this article, so... this is going to be based significantly on my own observations and "collected knowledge", although this article (thanks, Ken!) has a remarkably similar take. If you want a laundry list, read the aforementioned article. I, personally, believe the most serious problem is:

Compromise

To explain, consider several major problems:

Naturalism is a philosophy (read: "religion" by another name) whose central dogma is that God does not exist. You are likely most familiar with this philosophy due to its twin spawns of Evolutionism (the claim that all life originated as a result of random processes, that humans are not materially different from beasts, and so forth) and Uniformitarianism (known primarily for claims that the Earth is billions of years old). These claims are being shouted at "westerners" constantly, with their supporters insisting that they are "indisputable, proven facts". These "facts" stand in direct contradiction to the true and God-breathed history of the bible and undermine the very foundations of Christianity. (Evolutionism, in particular, is directly at odds with the doctrine of Original Sin.)
Relativism denies that there is such a thing as "truth", particularly with respect to morality. Under the guise of "tolerance", it vilifies (that is, is intolerant of) those who try to cling to traditional Christian morality. In the absence of "truth", there is little reason to remain Christian, leading to the related issue of Universalism. (I'm reminded of an article about many young people in the UK converting to Islam precisely because that religion remains firm in its convictions.)
Secularization of worship is seen in many Protestant and non-denominational churches, particularly "mega churches". Not unlike the previous point, attempts to cater to "the masses" and "engage the emotions" result in a "watered down" Christianity that loses its ability to connect people Spiritually to God.

The common thread in all of these is compromise; namely, rather than standing firm on Christianity's historical convictions, many churches are giving in to cultural pressure to conform, to achieve "consensus" with secular groups, and are thus allowing the foundations of Christianity to be undermined. When "Christianity" looks just like agnosticism, why bother to be Christian? When Christianity gives up its foundations in the name of "tolerance" and "science", it becomes the proverbial house that was built on sand, unable to withstand the attacks of the world and the adversary. "Christians" lacking those firm foundations are readily overcome and fall away.

The problem isn't just with individuals, either; when these attitudes infest a large number of Christians, church bodies suffer as well, for much the same reasons. One of the previously mentioned articles speaks of "lukewarm" Christians thusly:

Lukewarm Christianity teaches Christians that compromising our faith is acceptable. Instead of standing for righteousness, lukewarm Christianity encourages the body of Christ to remain neutral.

When the body of Christ becomes neutral we also become ineffective. In addition, we relinquish power and authority to those who wish to change the standards of righteousness to fit their own agendas.

A lukewarm church aids the agenda of the enemy without even knowing it.

Compromise thus affects both the individual believer, by robbing them of the strength to withstand the assault of the Adversary, and by robbing the greater body of Christians of the ability to stand together to support those believers that falter. Meanwhile, the failure to stand up to the forces arrayed against the Church lends strength to their assaults.

Many westerners may believe that we are free to believe what we want, but in truth, persecution of Christians is thriving. Educational institutions in particular have been shoving Naturalism down children's throats for decades (and are starting to push racism and Marxism), as this article notes:

While music, entertainment, fun and games may ultimately make church an exciting and interesting place to be, it is the foundational intellectual challenges and doubts about the Christian faith and the Bible that are not being answered. And there is nothing more foundational in the Bible than the early chapters of Genesis—the very chapters that will be attacked the most by secular, higher education, particularly in the sciences where evolution is taught to the exclusion of everything else.

...and later:

We are not saying that creation vs. evolution is the only reason our youth leave the church, but our surveys clearly showed it is a major reason.

If Christians are unwilling or unable to fight back, is it any wonder our numbers are dwindling? The Adversary knows where to hurt us; if we fail to hold fast to what is true, and allow ourselves to succumb to the siren calling of anti-theistic world views, how can we stand?

What can be / is being done?

[Note: the quoted part of the question below was subsequently removed to make the question more focused. However, the following still seems useful, so has been retained.]

What measures (if any) are Christian churches taking to counteract these reasons for deconversion? Do any Christian churches or organizations teach people how to have an unshakable faith, even in the face of the most challenging objections?

Unfortunately, a lot of churches are part of the problem. Not all, however; some churches are still willing to teach the Truth plainly, but they are an unfortunately-dwindling minority.

As for organizations... the outlook is a little better. Here, I have an admittedly non-mainstream view, which is that the fundamental issue is Naturalism. Secularization comes mainly from a misguided desire to "be appealing". Relativism is in many senses an outgrowth of Evolutionism and Naturalism, since the denial of Truth rests ultimately on denying God. Once God is allowed in the picture, the case for Relativism is significantly undermined. Similarly, if churches were to hold firmly to doctrine, I believe they would naturally recognize that doing so is the best way to retain membership, and secularization would die a natural death.

To ask the favorite question of a prominent theologian: What does this mean?

In many ways, I believe the problems with Christianity today all stem, ultimately, from rejection of one premise:

In the beginning, God created the heavens and the earth.

When one realizes how pear-shaped things go when this foundational truth is rejected, it doesn't seem like much of a coincidence that this is the very first verse of the bible.

When a Christian acknowledges God, he or she must reject Relativism. When one allows for (and accepts) God's existence, one can recognize and reject the vaporous Holmesian fallacies on which Naturalism has built Evolutionism and Uniformitarianism, and can recognize how a historic reading of Genesis is a better fit than these man-made delusions (n.b. 2 Thessalonians 2). With such an understanding, one has a firm foundation and is equipped (n.b. Ephesians 6:11) to withstand the anti-theistic and false teachings of the world.

Some organizations that are trying to take this on, and have many, many resources to help Christians stand firmly on the foundations of Genesis 1, include:

Matthew 5992

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Although I would agree with the previous answers that philosophies stating axiomatically that God does not exist are constantly undermining the efforts of churches and offering false alternatives to the Christian worldview, I would approach this question from a slightly different angle.

I believe the chief cause for falling away is the erosion of the understanding and active teaching of the main Christian message, the Gospel (which means message / good / important news).

To be clear (and not to do what I’ll describe later!), what I’m referring to can be stated in a number of ways, but let me state it thus:

God is the loving ruler of the world
He made the world, and he made humans to rule the world, and to be under his rule
But humans have rejected God’s rule, and instead want to rule themselves. This has fractured the relationship between us and God.
Now God is completely just, and must punish the rebellion. But he is completely loving also, and wants to forgive and heal.
So he sent his son Jesus into the world, who always lived under God’s rule. Yet, when he died on the cross, he took on himself the punishment that is due to us all for our rebellion.
Furthermore, God raised Jesus from the dead, and made him the ruler of the world.
Which leaves us with two ways to live (the title of this Gospel outline, actually): either, we can continue to rule ourselves, facing punishment and death when we die, or we can accept the rule of Jesus - with the forgiveness and life that brings - a richer life now, and eternal life after we die.

Now there are three categories into which a church can fall regarding this message:

Gospel taught: This message, or an aspect of it, is explicitly explained and unpacked at every meeting. E.g. in the account of Jesus calming the storm:

“Jesus is the ruler of the waves, of the natural environment. He is the king of creation and can calm not only the storms of nature, but of your life too, if you accept his kingship. Accepting his kingship makes you right with God again, and if you were to die on your way home, you would find there had been much more restored than just the storms of your life. Jesus is the king of the whole universe! He is is the radiance of God’s glory. Submit to him; receive the gift of eternal life!”

[There are (perhaps obvious) reasons why one can legitimately spiritualise the story but I won’t go into these here.]

Gospel assumed: The Gospel message is believed, but if you were a young believer, or sitting on the fence - or simply needed reminding! - you would hardly ever hear it in the church’s teaching. In our same story, e.g.:

“Jesus can not only calm the storms of nature, but of your life too. Why not accept him as Lord of your life? Ask him now to come into your life, so that you can have restoration too!”

If a church ceases actively to keep spelling out the Gospel, it becomes an assumed truth, and the church can easily slip into the third category:

Gospel lost: The main message of the Bible, the very promises of forgiveness and eternal life, have been lost from the teaching of the church. Our example one more time:

“In this story, Jesus calmed the waves, and the disciples were amazed. How can we, today, invite Jesus to speak calm into our lives, into our stressful situations? Let’s pray to Jesus now, breathing deeply, asking the Christ light to come into us… bringing peace… bring calm… bringing love… bringing light.”

This third category might sound like an overstatement but let me assure you, there are many many churches out there today where you will hear nothing but this kind of airy gumpf. A person sitting under this teaching has no hope whatsoever of hearing the true Gospel - unless of course they were to pick their Bible up and start reading it in chunky sections. But if they didn’t do that, they might well eventually give up on their church, and possibly on Christianity also - without ever really having understood the Gospel, or how to respond to it, in the first place.