It's not just the stance toward homosexuality. It's a lot of things. I don't have a problem with religion on its own, but blind, unquestioning adherence to it can be problematic. I'm not vilifying or dehumanizing anyone. Quite the opposite, in fact-- religious adherents have brains, and they should use them to think critically about what they're taught in church, not just accept it blindly. Some do, of course, but I would say that at least in the US, the vast majority of the religious right do not. Lark, I know you've thought critically about your beliefs, and although I still disagree with some of the beliefs you hold, I can respect that you have a right to your own opinion.
As for the Bible thing, again, I think that has to do with critical thinking. You don't believe in all of it, if I understand you correctly. That's exactly how I feel-- some of it is true and relevant, some of it is blatantly wrong. It's just that in the religion I was raised in (Assembly of God) we were taught that you can't pick and choose what parts of God's word you believe, so even now, after having rejected that religion, I have trouble with the idea of only agreeing with some parts. That's really more where my conflict comes from... the issue with homosexuality is only ONE of the things that the Bible teaches that I believe is blatantly wrong. There are many others. I don't know if what you say is correct, that religion isn't historically responsible for the taboo against homosexuality. You are better versed in religious history than I am, so I'll take your word for it. But be that as it may, I don't find history particularly relevant to this argument-- some (many) religions
nowadays specifically teach that homosexuality is wrong, and today is what concerns me.
From my early religious education: God exists and is perfect and all powerful. He doesn't make mistakes-->The Bible is God's Word. It was written by men, but dictated by God.-->God wrote the Bible and he doesn't make mistakes or change his mind, therefore everything in the Bible is and always will be true and relevant.
My critical thinking: Some teachings in the Bible are true and relevant; others are ethically wrong.-->Therefore, the Bible is not infallible nor timeless.-->Therefore God must not be perfect.-->Can an imperfect God really exist?
See what I mean?
EDIt: To add this part:
As for the "I'm right, you're wrong" thing, my line of work is all about teaching respect for cultural difference. I am, again, all-or-nothing on that one. It's easy to respect that people of other cultures like different foods and wear different clothes. It's a bit harder to respect their different way of going about education, personal distance and or hygiene practices, etc. It's really difficult to respect the treatment of women, systems of justice that are drastically different from mine (sanctioned murder, etc), but again, my personal code of ethics and beliefs doesn't allow me the arrogance of saying where the line between "Different" and "wrong" is. Of course I don't CONDONE the treatment of women in Afghanistan, or sanctioned murder, or things like that. I don't respect the practices themselves. But I respect the right of a culture to determine what is or is not appropriate for themselves.
For example, in the US, we have decided as a culture that driving on the right side of the road is appropriate for ourselves, so our traffic laws were based upon that. I understand you do things differently in the UK and Australia.

It feels totally foreign and unnatural to me when I'm in those places, and I have to be really careful not to get hit by cars when crossing the street, but I'm not going to tell you it's wrong.