Her article is worth the read. And so are the comments. Here is one by Billy the Bloggin Poet which sums up the problem succinctly:
The answer is in-fact simple but sadly not easy. The only way harmony can be achieved is when everyone sees God the way I see God.
Okay, you know that ain't right but that is exactly the problem. There's nothing wrong in believing in God-- any god. There's nothing wrong in not believing in a god. Belief is simply something people have. Our beliefs are not the problem. Belief does not equal sin-- never has, never will.
The problem is in-fact inherent in EVERY religion that has ever existed: Every religion, no matter how tolerant perpetuates the idea that other ways are wrong. If religious leaders were to teach us to be open to other ideas they would be teaching themselves right out of their jobs. After all, without religious controls you've no need for religion. Religion is a self-fulfilling prophecy, its motive not to save men but to save religion. As long as religion continues to exist this fighting between the various religious and non religious groups will continue.