It has everything to do with the ideology of evangelism, which, unfortunately for non-asshole Christians, is specifically of a Christian bent in this country. (Can you imagine if an atheist student tried to drum out a Christian professor? My god, this would be national news.)

Bottom line: any dogma that causes you to act contrary to the best interests of people other than yourself is bad. The fact that religious dogma is particularly difficult to confront and shut down (without being vilified in turn) is the problem, not religion itself. Indeed, our recognition that religion is (for the majority of people) important is what keeps a lot of people from speaking out for fear of being assumed to be a bigot when they're really just griping at that one particular person/group using religion as a cover.