What is the biblical and early church basis against religious tolerance?

The arguments in favor of church intolerance needs to be analyzed in relationship to the early church's appearance of being tolerant towards other religious viewpoints. These arguments run as follows.

At the end of the Book of Romans 16:23, “Erastus” is mentioned as the οἰκονόμος - i.e. as the NIV puts it, the “city’s director of public works.” It is interesting that this position, by definition of the nomenclature of its Roman office, would have likely required a fiduciary responsibility to oversee the funding for the maintaining of idols and temples in which promiscuity took place. These places involved the very activities that the Apostle Paul was trying to get people to leave behind. As Brad Kirkgaard in his article "Rendering to Caesar and to God: Paying Taxes in the Roman World" points out:

In a world in which the favor of the gods was seen as essential to the success of Rome, much of religious life was closely linked to the state. It is no surprise, then, that tax revenues helped to support a range of temples and festivals. Indeed, a fitting expression of this religious connection is offered by the central location in Rome of the Temple of Saturn where the tax revenues were kept.

Thus Erastus' duties as treasurer of Corinth is an N.T. example of Christ & culture in paradox - i.e. where a person pays taxes that ends up directly or indirectly supporting funding of certain organization that conflict with one's value system.

Tertullian wrote in 212 A.D.:

...the religious practice of one person neither harms nor helps another. It is not part of religion to coerce religious practice, for it is by choice not coercion that we should be led to religion.

In his tract Divine Institutes Lactantius wrote:

The worship of God . . . requires full commitment and faith. For how will God love the worshipper if he himself is not loved by him, or grant to the petitioner whatever he asks when he draws near and offers his prayer without sincerity or reverence. But they [the Romans], when they come to offer sacrifice, offer to their gods nothing from within, nothing of themselves, no innocence of mind, no reverence, no awe. . . . [Religion] cannot be coerced. It is a matter to be dealt with by words not by blows. For it has to do with the will.

Athanasius taught that "Truth is not proclaimed by swords and missiles, nor by means of soldiers, but by persuasion and counsel.”

Back around 380 A.D. Gregory put it this way:

I do not consider it good practice to coerce people instead of persuading them. Whatever is done against one's will, under the threat of force, is like an arrow artificially tied back, or a river dammed in on every side of its channel. Given the opportunity it rejects the restraining force. What is done willingly, on the other hand, is steadfast for all time. It is made fast by the unbreakable bonds of love.

Centuries later, St. Bernard's rule, Fides suadenda, non imponenda ( "Faith by persuasion not by violence") reflected this conviction.

All the above needs to mentioned, as all good arguments need to address the strength of opposing positions. The argument against being tolerant is that later on in Christendom, with the collapse of the Roman Empire, there was a need for its replacement to function as a type of in loco parentis. This implied a belief that the Holy Roman Empire had a right to be intolerant towards anything that hindered the freedom for effective Christian parenting to take place. For example, one might argue that the Council of Nicaea led to the state suppression of Arianism.

One author notes the following:

In 325 Constantine convened the Council of Nicaea to settle church doctrine and then issued an edict banning heresies. In 385 a Spanish bishop, Priscillian (c. 340–385), became the first person to be executed for heresy.

St. Augustine of Hippo (354–430) was the most influential theorist of persecution. After belonging to the Manichaean heresy in his youth, he joined the Catholic Church in 387 and eventually became a bishop. Facing Manichaean, Pelagian, and Donatist heresies, at first he advocated peaceful methods but by about 400 he began to endorse coercion. He interpreted the parable of the tares (Matt. 13:24–30) and the parable of the feast (Luke 14:21–23) to justify coercion of heretics.

For a more scholarly analysis, see the dissertation by Mary Imparto on Religious Toleration: Prudence and Charity in Augustine, Aquinas, And Tocqueville.