You have a good point about there not being a word for hating a religion. So, I propose a new term: "Theophobia", discrimination against a group of people for their religious views.
As for my views, I'm a rather ardent Christian, though some of my views on particular issues do alienate me from the rest of the church (To be fair, Jesus suffered from the same problem).
As for religion in general, I consider religious organizations, even ones with views I disagree with (Buddhists, Muslims, Hindus, ect), as a necessary part of civilization. You simply cannot underestimate the power of religion, and I believe the groups that have tried to harness that power have mostly used it for the betterment of mankind.
Also, I tend to think that a religious extremist without religion is still an extremist, and now doesn't even have religion to restrain them, as a religious extremist at least limits himself to perceived enemies of his religion.