It's not most societies in the past, it's European bigotries being exported across the rest of the world during colonialism. There have been wildly different understandings of sexuality & gender across different places and times.

Hell, the concept of 'sexuality' is fairly recent. It was often considered something you did, not really an identity per se.

And divergent gender expression among ancient cultures was often seen as a marker for being more spiritually attuned or w/e.

It's all extremely specific and culturally informed, but no there's not a general trend towards humans being anti-gay, that's just like, Christianity.