They are looking at the more strict and fundemental parts of religion. I have to admit that I understand why they'd dislike religion (I'm an ex-Christian), but there is no <<correct way>> of reading a holy text, interpreting it and practicing it (despite what ppl say). You can practice religion in the way that makes you most comfortable and confident and there will still be queer ppl that'll like/love you.
Honestly, if you lose friends because of your religion, they weren't true friends. Best to cut them out of your life anyways.