This is a many faceted issue. I shall elaborate on a few points. There are many more than the ones I am listing. All of the points I would have made about why lesbians are much more tolerated have already been made, hence, I shall focus on the objections to gay men.
Some heterosexual men have a hint (or more) of bisexuality in them and the very existence of homosexual and bisexual men threatens their own identity. For them it is a matter of “he doth protest too much.” If a woman hits on a straight guy and he is not interested, he will turn her down, usually nicely. If a gay man hits on a straight guy, the straight guy is going to respond anywhere from a very nice “no thankyou” to beating the everloving crap out of the gay guy. I have never heard of a woman who hit on a straight guy having the crap beaten out of her for such an action. I believe that the stronger the negative reaction, the more likely the man is to have some, shall we say, leftward leanings.
Another issue is the Church. In many nations over the years, male homosexuality has either not been frowned upon or even revered. However, in the very Christian America, the Bible has been interpreted to say that homosexuality in men is a sin. I am, by no means, knowledgeable in the Bible but I have never heard of a passage being cited as saying that homosexuality in women is a sin.
Here is another one, something that my lovely Keysha just explained to me. I do not know enough of the history of matriarchal societies to verify this but it makes quite a bit of sense. In patriarchal societies, such as America, men have, for centuries or even longer (in nations older than America), been considered the dominant/ better/ otherwise superior gender. Women, for much of that time, were (and, sadly, are in some nations) treated as lesser beings and/or as property. As is seen in this thread, gay men are often associated with being feminine. Thus, men who act, in the minds of their contemporaries, as feminine, destroy the myth that men are the superior, stronger gender.
From my observations, many homophobic men seem to be on the insecure side. I am not talking about people who disapprove of male homosexuality, rather people who hate gay/bi men. There is a difference. I am bisexual and have quite a few straight male friends who, while they disapprove of homosexuality/bisexuality, have no problem with me. We just agree to disagree on this one thing. They do not find me threatening. However, I have been blasted and attacked by others because, from what I can tell, they perceive me as a threat to themselves and the moral fiber of this nation.