From what I've observed, the more homophobic a person is, the more likely they have homosexual tendencies and scared to admit them.

Not surprisingly, the most religious of societies have the least tolerance of human sexual behavior that does not conform to the standards of their particular faith. These groups teach the young that these behaviors are abhorrent and should be met with severe punishment. Therefore this hatred is learned behavior. We don't grow up hating by nature, but rather by the influences of our particular environment.

Society sets social norms. Consider the ancient Greeks...homosexuality was accepted by society and therefore individuals accepted it as well. People are generally sheep who will go along with whatever behavior they perceive everyone will accept whether harmful to others or not.

Some of it may just be surface, peer-group hate-mirroring, but when people are homophobic on a deep, emotive level I generally assume they are in conflict with their own inner homoerotic feelings.

An aversion to unnatural concepts may come from how messy the idea may get in the ideas of cleanliness for sodomy. We do know how many diseases can result in the colon. Then there is the accidents of doing the act. The cliché of packing chocolate so to speak or losing the chocolate uncontrollably. The idea of cleanliness is next to the deity is not unique to any one religion. It seems to be an abstract of disgust with the potential problems. In societies that practiced sexual acts more openly it was less taboo but you still ad the potential accidents that were just not cool to many people. Sexual pleasure is one thing but being defecated on was another problem.

The idea of altering the sexual identity from what it born into is relativity new. The idea of the girlie man and masculine females have been expressed in genetics for a millennia and we understand it from a hormonal concept. However, the idea of physically changing the sexual identity is relatively new. This makes it hard for a lot of people to understand why an individual may want to change from their natural born state by surgery. What people do not understand results in fear of the idea and hatred to spread. The idea that certain clog has specific definition for women and other clog for men has never set well with me since clog is the art of expression of the individual when one gets far enough in evolution of the individual's mind.

I would think a lot stems from religious view that merged into society. I live in Florida 10 years ago my home town was country and there was maybe 1 or 2 gay kids in school. Of course they were picked on as such things back then were taboo, now times have changed and it's more accepted by society as a whole but some still carry the views of their parents or older siblings. A majority of people are always going to be standoffish from someone than has a completely different view on life and how it should be. To be honest I didn't want to even associated with someone who was gay or other preference when I was younger but now I have 1 homosexual friend and 3 bi/lesbian friends some people will realize they are still human beings with their own rights and other will always look down upon them. As far as plants and animals are concerned we are still part of the animal kingdom so I would think that it is probably hard wired to a majority of people due to if everyone was gay/trans ECT. their species would most likely die out, but there is a case of a lizard I do believe it indigenous to Australia that is only female and reproduction is stimulation by another lizard rubbing them in the right spot, point being I think regardless life will always find some way to continue, but for all of nature the #1 rule is preservation of your kind so I would think the workings of this world would play a major role in peoples thoughts

Good question, there must be some research on this somewhere. I'd think a combination of factors, but I expect more familial/societal than innate. that's just a layman's observational conclusion, but I've seen attitudes change over the last 60 years, & I know historically that gays were more accepted in some cultures more than others, so that's my take. From the outside, so to speak, so someone gay may have a different viewpoint.

Probably a variety of reasons.
Most based on fear, misguided ideas of gender, religion, latent homosexuality manifesting/projecting.
No simple answer really.