As you suggest or hypothesize.
I agree that it's sexism, albeit a kind of sexism that gets a lot less airplay than sexism against women.
I think that the anti-gay/homophobic aspect is way overblown. For one thing, this "less than a man" thing happens with other forms of victimization or even simple injury without someone to blame.
It starts quite early. Boys who are injured on the sports field are told to man up and just take it. Occasionally, there is a component that can be linked indirectly to homophobia, where the boy is called a "sissy" or something. However, even in the absence of this, the training happens.
Actually, it happens earlier than that. See
http://www.jstor.org/pss/1128199 It's only the first page, so I had to look it up in a university library. Basically, a bunch of adults were shown an infant engaging in a certain behavior. They were then asked to guess the emotions of the child. When told that the child was a boy, they overwhelmingly answered "anger," and when told that the child was a girl, they overwhelmingly answered "fear."
To me, the most interesting part of the study was that there was no correlation with the political beliefs of the adults. That is, progressive, gay-positive adults were just as likely to make those sexist judgments.
So, while one can make a plausible homophobia connection with some of this, it is more than a bit of a stretch to consider it a definitive explanation.
A better explanation (one popularized by Warren Farrell) is that males are conditioned to be soldiers, while females are conditioned to be caretakers. This receives support from primatology. Even in primate societies such as those of baboons (largely matriarchal, and in the case of the Berkeley baboons, strongly matriarchal), essentially all young males and most older males are relegated to be at the periphery, providing defense against outsiders. Relics of this exist in human societies. Most armies are overwhelmingly male, and except in cases like Israel for a brief time, involuntary conscription for combat is exclusively male. Even when armies are wholly volunteer, they rely on a steady supply of conditioned males. So does business.
Now, we could go a lot further and ask why this is, or rather why we as humans haven't gotten rid of it by now. I don't know. The answers are probably complex, and at this point, there is even less room for a homophobia explanation.