Fun fact: the bible isn't actually explicitly homophobic, it's just that people started misinterpreting lines of it and using said lines as proof that homosexual people were bad and as a result, people began thinking Christianity was homophobic when in reality, it was just that some of its supporters were.
That's completely aside from the point, though. What I was going to say is that religion is inherently flawed, as is atheism. There's no perfect religion, and as long as you can accept that and still respect others' religions, you're cool in my book.