The argument seems to go something like this:
We should respect one another's world views
My world view states that certain people are diseased and should not have equal rights
It is inappropriate to state that my position is itself the result of disease, as that does not respect my world view
Certain people have suggested that the term homophobia is inappropriate because it marginalizes those that are opposed to gay marriage. Yet these people themselves see no problem marginalizing gays by denying them the right to marry--and many of them want to see gays institutionalized, accusing them of having what they call "same-sex attraction disorder." And so their argument eats itself. If it is okay for you to try and deny certain people the right to marry, it is okay for me to say that the problem is with you and not them.
Research seems to suggest that the reasons behind the anti-gay movement are indeed rooted in fear:
Not all people who oppose gay marriage necessarily experience anxiety in the presence of homosexuals, but they are a part of a movement that has this anxiety at its base. Some people actually experience this anxiety (to one degree or another), whereas others simply follow the lead and rationalizations of those that do. But groups work in interesting ways. "The larger the lynch mob, the more brutal the lynching." What may be only a little anxiety on the individual level compounds in the presence of a group. A group may end up acting far more violent and fearful than any of its individual members.
The term homophobia, like the term xenophobia, has larger social implications than simply what is happening on the individual level. Cultures can be phobic of other cultures--that is to say, one group can show an aversion to or even an antagonism against another. While this is rooted in fear--one group experiences the other as being in some way a threat to it--the influence of this fear may be transmitted to the individual members of the group in any number of ways--even dispassionate rationalizations or religious dictates. "While the phobic person is aware of the aversion, even hatred, of the target group they may not identify it or accept it as a fear."
If anyone can think of any reason other than fear as being the root cause motivating the anti-gay movement, let me know. I can't see any other basis for it.