I think that another reason (though it's been touched on in a number of responses here) is the fact that the human population no longer depends on just the "fittest" as it might in populations of other animals where natural survival ability dictates far more which individuals will live to pass on their genes. Human beings, especially in this day and age will tend far more to nurture and protect the weaker and less able. Not that this has anything to do with homosexuality, per se...just a notation of the fact that there is far, far more diversity in the human population than in wildlife, and very probably far more diversity in the human population in this day and age than in the past.
As others have said, also , there is a really wide range of sexual behaviors and preferences, and it's really all on a continuum, where a lot, maybe even a majority of people will fall somewhere outside of being (or at least feeling) exclusively, 100% heterosexual, 100% of the time. I think many people might be reluctant to even admit to or to examine within themselves. And as such, I think, there is nothing inherently "wrong" about them.
On the other hand, the issues of the preferences which are really out in left field, such as necrophilia, bestiality etc, are a really unfortunate offshoot which luckily does not affect more than a tiny percentage, and is probably exacerbated by environment or brain chemistry. Also, and I might be wrong, I think some of these things might show up more in the sociopathic personality, which is another question altogether. Maybe some of these tendencies might have been "weeded out" to some extent in the past in various ways ranging from execution to sterilization, to institutionalization beyond redemption, but there would still be carriers in the population (if the causes were, indeed, genetic), so I'm not sure how much of an impact that would have had. Anyway, it's the tip of a "slippery slope" argument to say some of these things are on the same continuum as homosexuality, and I'm not going to go there. Some may well be, but if the tendency involves hurting or taking advantage of another individual or innocent creature as opposed to simply allowing certain individuals the same rights to create a loving family structure as others, it's not the same thing at all.
Also, there are cultures which do embrace homosexual/tansgender personalities as alternate "sexes", and recognize their contribution. I don't doubt but that there are a lot of things which more feminine males and more masculine females can contribute to a society regardless of who they actually choose to sleep with.