Well, the Crusades were a major contributing factor. They started off as a noble enough idea, reclaiming the Holy Land for Christendom. Trouble is, there had been Christians living in the area since, well, 33AD or so, and they seemed to have a pretty good handle on looking after such Christian holy sites as the Church of the Nativity and the Church of the Holy Sepulchre…
The Crusades quickly degenerated into a land grab by second and third sons of European nobles who, due to the primogeniture laws, weren’t going to inherit much of anything from their fathers. So, hey, there’s a fair amount of land in the Middle East and North Africa, so they went off to carve out fiefdoms, duchies, even kingdoms for themselves.
Needless to say, the locals were pissed, and being that the vast majority of the locals were Muslims, they saw (partly correctly) the invasion as an invasion of a foriegn religion (infidels in their eyes, although the Koran does not regard Christians and Jews as infidels).
By the end of the thirteenth century, the Crusades were becoming a thing of the past, but the situation had rise to a lot of Islamic fundementalists who, understandably wanted to preserve their way of life from the foriegn Christian invaders. Like many of their modern fundementalist Christian counterparts, they came to regard scientific knowledge as leading people to deny faith (Jerry Falwell, anyone?), which, from the fourteenth century on, led to a major decline in the sciences and medicine.
Of course, European colonialism during the eighteenth and nineteenth centuries didn’t help the situation any…
Hope that helps.