Not the person you responded to, but I'd like to take this one.

I'd say it overwhelmingly comes from two sources: the environment that you're raised in, and innate human tribalism.

The first is pretty straightforward; if you're raised in a racist or homophobic or misogynistic culture, there's a good chance you'll adopt it too.

The second is more interesting, and probably the original source. We have a lot of habits that made sense for our ancestors 100,000 years ago, but are useless or harmful now. It doesn't really benefit us to crave sugar in a time that it's widely available in unhealthy amounts, or sit down and conserve energy in a time where food is plentiful. Similarly, it might once have been useful to see another tribe of people that are different from you and have innate suspicion or dislike of them; there's a good chance they could harm you and your tribe if they're trying to take over your hunting territory or whatever. Now, though, this just leads us to pick up any difference we can between us and use it as a divide. Thankfully, a lot of us have managed to suppress this to the point where we'd never even consider acting on it, but some people just aren't there. And if they're in a culture that doesn't encourage that suppression, they probably never will get there.

Religion is just the excuse some people give to justify their behavior. Take it away, they'll come up with another. There are people that argue that homosexuality is not supposed to happen from an evolutionary perspective because it can prevent you from having kids. Or there were all sorts of pseudoscientific experiments in the past centuries that set out to prove that women or black people or [insert discriminated group] had worse brains than white men. Or it could even be economics; blaming the Jews for economic recessions or whatever.

After all, somebody wrote those lines in the Bible. It's not like the religion spawned from nothing and introduced racism to the world.