I've been listening to a series of lectures by Professor Frederik Gregory. One of the interesting points he makes, a number of times during the lectures, is that research by historians of science has shown that the idea of a long-standing conflict between religion and science is something that has been read back into the past by modern intellectuals. Of course, there were incidents where some particular scientist ran afoul of some particular religious body (like Galileo). But, basically, until the mid-19th century, just about no scientists or religious people understood the two to be at conflict in some fundamental way. Most scientists talked of how their findings "showed the glory of God" -- and for the most part, this was not just for show, as most of them were genuinely devout. (Newton, for instance, spent more of his life on Bible studies than he did on physics or mathematics.)
Furthermore, Gregory notes, the change in this view did not originate with science, but with the political radicals of the mid-19th century, who persuaded the younger scientists of the time that to be "progressive" one ought to be materialistic and atheistic. It was only then that the exact same sort of findings that, a generation before, would have displayed the glory of God, now were seen as indicating his non-existence!