I just read your question in the Slate article (www.slate.com/id/2174411) that asks sex columnists what puzzles them. For you, it was, in short, "Why homophobia?"
I'm convinced that boys learn it from their peers. Once a person is labeled gay, that person is marked for ostracism. A boy who comes to the defense of a gay boy pretty much guarantees that he'll be lumped in with the gay boy, so a powerful taboo is set up. If he joins in the ostracism, he'll be rewarded with membership in the brotherhood of dudes.
I'm sure I'm just touching on the situation here, and it's sort of a chicken-and-egg solution, because who taught the meanies homophobia in the first place? And finally, I'm from Hawaii, where folks are a tad more tolerant of gays. It's not a Shangri-la of acceptance, but Hawaiian culture is more inclusive than mainland American culture. So I guess I can end with another question: why are some cultures more homophobia prone than others?
Yes, I was asked come up with something that I just don't get, and I picked homophobia, or rather, the kind of semidispassionate, delayed-gratification, frighteningly organized sort of homophobia that results in antigay marriage legislation, not the kind that results in broken heads. The latter I can understand, sort of. The people who break heads with their inarticulate, reflexive need to Hulk Smash! whenever they feel their shoddily constructed senses of self crumbling at the margins are not the people who coolly invent laws to ruin other people's lives from a distance. Those are the ones whose motivations fail to connect with me, so every time I try explaining them to myself (they sincerely believe their gay neighbors are breaking God's laws and must be punished; they feel very strongly that only heterosexual marriage can protect Western society from the barbarians at the gates; they want to save Ellen and Portia from sin; etc.), the brief, bright light of understanding flickers out, and I find myself wondering why those people will not go away and leave the rest of us alone.
It's not that I'm entirely at sea as to where homophobia comes from or why people feel it. I believe quite strongly that we are wired to be exquisitely sensitive to sameness and difference and that once upon a time recognizing one's own was a vital survival strategy on the Serengeti, as anything strange was far more likely to be foe than friend. I also believe that humans evolved with an extraordinary gift for pattern recognition and an accompanying discomfort around things, especially people, that fail to categorize neatly. Just ask any transgender person or any parent who has been subjected to the surprisingly aggressive grilling that old biddies on the street feel entitled to initiate: "Are you sure she's a girl?" "Yes, quite." "Then why is she wearing a blue hat?" People are extremely invested in knowing who's a what and who isn't. This maintains order, and we are order-loving animals. Obviously how order loving varies: compare, if you will, the behavior of Israelis attempting to board a bus with that of the Swiss those kinds of small variations probably account for the slightly less homophobic milieu of your island home, if in fact you're not imagining it.
We know these things about our primitive behaviors, and we know that, like violent sexual jealousy and rape as a reproductive strategy among many other unattractive behaviors from our prehistory they're no longer adaptive.