Homophobia, like xenophobia, is rooted primarily in fear of the 'different', dislike for the unlike. Humans being a pack species by nature, and predatory to boot, anything seen as outside the norm, not of the herd, will be viewed with distrust leading to hatred if unchecked. Throw in a few self-appointed leaders to foment that hatred for their own aggrandising ends and you have a very volatile mix. There's nothing about evolution, properly taught and understood, that leads to anything like that, which is probably why those leaders and similar parasites need to distort it to give themselves a veneer of justification.
At the age of five, Skagra decided emphatically that God did not exist. This revelation tends to make most people in the universe who have it react in one of two ways - with relief or with despair. Only Skagra responded to it by thinking, 'Wait a second. That means there's a situation vacant.'