The difference lies between atheism and antitheism. If you're saying that anyone who worships their "flying sky daddy" (lol) should go to jail, well, you're making atheism your own dogma, therefore committing the exact fault intolerant religious people commit. Atheism is not a religion. Antitheism is. I'm not sure it's perfectly accurate to define antitheism as extreme atheism, but it could be seen like that.