Simply stated, the real reason that some atheists hate religion is, they are more into theism than they think.

An atheist turns his back on the idea of God so that he can live his life according to his own dictates. Often that life is in conflict with the things that God teaches. An atheist who has trouble pushing the idea of God or theism out of his mind, hates religion because it conflicts with the way he wants to live, and he doesn't like feeling guilty or even borderline guilty. In truth, he hasn't pushed the idea of God out of his mind as successfully as he has thought.

Some atheists are not like this. Some have pushed theism out of their lives so successfully that they don't have the conflict. They can listen to people talking about God all day long, and it totally doesn't affect their conscience. Usually these kinds of atheists don't hate the religion. They simply get disgusted with theists who get in their face. And, they often get disgusted with other atheists who believe in a different form of atheism than they do, and get in their face like the theists do.