The Enlightenment didnt start out being against all religion (though it was always anti-Catholic). Some of its exponents were Anglicans, including William Paley, whose Natural Theology (1802) is still one of the basics of Intelligent Design (from finding a watch, we infer the existence of a watchmaker). Yet the views of most Enlightenment thinkers almost inevitably led them away from being orthodox Christians, normally towards being Unitarians, Deists or atheists. There seem to me to have been several reasons for this.
One was the demand for rational religion. Enlightenment thinking wanted nothing mystical or miraculous. Religion was reduced to moral teachings and Christianity was held to be simple and natural. John Tillotson, who became Archbishop of Canterbury in 1689, claimed: The laws of God are reasonable, that is suitable to our nature and advantageous to our interest. For many Enlightenment thinkers, Christian theology and Scripture also had to be gutted to make it acceptable. The doctrine of exclusive salvation had to go: it was unfair to the virtuous pagans who had died before Christ. Many of the Bibles stories were held to be nonsensical or unedifying. (Roy Porter cites Thomas Woolstons Six Discourses (1727-1730) which complained that by cursing someone elses fig-tree Jesus had violated the sanctity of property!) All this tended to be accompanied by the usual condescension towards the masses: there was often a Double Truth theory by which the Christian revelation was merely to ensure that Gods message reached the masses, while to the enlightened religious truths were obvious.
In particular, during the Enlightenment the divinity of Jesus increasingly came to be rejected (as by the Unitarians and Socinians). I suspect the main reason was that the entire doctrine of the Atonement no longer made sense in Enlightenment terms. If there was no sin, only ignorance, and humans were perfectible via education, then there was no role for Christ other than that of a Jewish equivalent to Socrates.
Enlightenment thought didnt just want to strip religion doctrinally, however. It was also extremely hostile to religious enthusiasm. This was initially a reaction to the fanaticism of the religious wars (English Civil War, Thirty Years War etc), which had produced a fine crop of extremist sects and doctrines and atrocities. But the opponents of enthusiasm went much further. Johnson defined enthusiasm as a vain belief of private revelation, a vain confidence of divine favour or communication. Any truly personal, emotional religion had to be rejected: not just Calvinism, but Quakers and particularly Methodism (seen as a mania or wild and pernicious). There was an inherent tendency in Enlightenment thought to see religion as madness. Porter comments: It fell to David Hume to complete the enlightened psychopathologization of religion. Meanwhile:
once madness was no longer attributed to supernatural powers, unbelievers like Dr Erasmus Darwin [Charles Darwins grandfather] could switch the blame for mass hysteria and religious mania to fanatics and Methodists and cast enthusiasm as itself a symptom of mental derangement. No longer did the Devil drive you insane: now believing in the Devil or in hellfire was, for physicians like him, a mark of madness.
Since Enlightenment thought was so hostile to religion, does that mean that Christianity must be inherently hostile to modernity? There are people now who seem to want to re-enact the battle, including some militant atheists and the Religious Right in the USA (who increasingly seem to want to reject all Enlightenment thought). I think there is a way, however, for Christians both to accept the benefits of the Enlightenment and yet to see its limitations. One is to accept the scientific method, while remaining sceptical about particular applications. There is nothing inherently wrong about the scientific method being applied to religion, as to any other aspect of society. But its perfectly reasonable to point out that the results are normally pretty unimpressive. Attempts at scientific history, for example, have been an overwhelming dead end. Meanwhile, a lot of evolutionary psychology has been incredibly sloppy (for example, by examining only one culture).
Secondly, Christians need to demonstrate the flaws in the ideas of inevitable progress or human perfectibility. I dont think this means going back to Thomas Hobbes view of the natural brutishness of man or even High Tory views of unchanging humanity. It is an advance that more people now believe that slavery is wrong and that women should have equal rights. But education is not simply going to remove error and ignorance from the world. Not everyone will be enlightened: not everyone will choose to be enlightened.
This leads to what seems to me to the biggest error in some of those who see themselves as the contemporary Enlightenment or Freethinkers. Christians are relatively able conceptually to cope with those who do not accept or reject Christianity. As well as those who have not yet heard the Word, there are those who hear it and reject it. (This is foreseen by Jesus, for example, in the Parable of the Sower). In some versions of Christianity those who reject Christ are automatically evil, but many Christians now would consider that those who do not accept the Gospel are not inherently more evil than Christians, but have some blind spot/hardness of heart. The virtuous non-believer/non-Christian is not an inherent contradiction.
In contrast, the Enlightenment model has no inherent way of coping with rejection. As Roy Porter puts it:
Modernizers were optimists; they thought in terms not of hopeless depravity but of problems to be settled. They prided themselves upon their benevolence and prized their power to bring improvement: those not enlightened were either innocents or victims. None was damned, none beyond rescue – education and philanthropy would allow them to enter the ranks of the civilized.
In this system, what happened to those who had received enlightening instruction and yet refused to become civilised in the Enlightenment sense (e.g. by obdurately sticking to their non-rational religious beliefs)? They could only be stigmatised: if a reasonable human, once educated, inevitably became enlightened, lack of enlightenment once instructed could only mean an inherent lack of reason in the person. There is still a tendency in some atheist thought today (by no means all) to regard any religious belief as a sign of madness, personality defect or incomplete mental development. The virtuous believer is a contradiction in terms for them. (At the most, they want religion allowed only between consenting adults in privacy). Christopher Hitchins , for example, was recently complaining about the childishness of believers (see http://www.slate.com/id/2135499/). Whatever you might think about Christopher Hitchins, you would look at him for a long time before the term adult springs to your mind. Christians ought to point out this condescending tendency when it occurs and enquire whether atheists really believe that the majority of the worlds population are deluded.