I just found a really informative blog post (by evolutionary Biologist Massimo Pigliucci) on why Science and Religion really do have problems with one another (read it here). I especially liked Massimo's quotation of Richard Feynman:
"I do believe that there is a conflict between science and religion ... the spirit or attitude toward the facts is different in religion from what it is in science. The uncertainty that is necessary in order to appreciate nature is not easily correlated with the feeling of certainty in faith."
In other words, religion demands that you have complete certainty in its concepts, while Science encourages you to realize you may be wrong, and to test your views constantly against others. These two ways of approaching the world are simply not compatible.