It usually refers to agreement. When someone is "for" something, that means they agree with it, want it to happen, like it, etc. If someone is "against" something, then they don't agree with it, don't want it to happen, don't like it, etc.
The answer is in your question. bible fundamentalist If you are a fundamentalist by definition that means you believe everything the Bible says in context. And then you ask. "Why do bible fundamentalists act like being against them means being against Christianity?" Do I really have to point out the irony of your question?