I agree with the AP's decision and rationale. I've always been annoyed with the suffix "-phobia" being tacked onto anything that someone else doesn't like. As the AP guy said, it assumes a specific motivation for another person's behavior; an assumption of information we don't have access to.
A phobia is a fear of something and, as Xelebes pointed out, generally a diagnostic term for a specific anxiety disorder.
"Disliking" something, no matter how strong that dislike, is certainly not the same as "fearing" it (I realize Weinberg, the guy who coined the term "homophobia," is a psychologist, but that doesn't automatically make his opinion correct. In fact, I disagree with quite a few things he's said over the years). If someone has agoraphobia, they have a very real fear of situations in which they feel there is no escape. If that same person has an extreme dislike of green beans or country music, we certainly don't say that they also have "legumeaphobia" or "twangaphobia."
I realize racism and hatred of homosexuals is not at all the same as hating beans, but the dislike motivating those attitudes is more alike to each other than they are to a "fear."
Sure, some people might harbor racist feelings because they were the victim of violence at the hands of someone of that particular race and being exposed to people of that race elicits a fear response. Indeed, I think it'd be safe to say that right after 9/11, a majority of US airplane passengers were at least apprehensive of, if not outright terrified by, any fellow passengers who looked Middle Eastern. The fears in both of those examples, though arguably misinformed, are at least understandable given the circumstances and, for most people, not the same as true racism.
I think for most bigots...the people who are true bigots...there's no fear involved at all. It's pure, dumb ass hate. Plain and simple.
I'd say that in most cases, some good ol' boy who hates blacks, or a black guy who hates Koreans, or a fundamentalist Christian who hates gays, or a Muslim who hates Jews, etc. doesn't hate them because he's afraid of them. He hates them because his closed-minded parents (and possibly preacher, family friends, etc.) has told him since birth that "those people" are inferior, stupid, smelly, lazy, worthless, going to burn in hell, and all other kinds of stupid shit.
Bigotry is taught. And bigots are taught to hate, not to fear. They hate because their daddy hated, and their daddy's daddy hated, and daddy's daddy's daddy hated, and so forth and so on.
So, calling their hateful attitudes a name that means "fear" is not only categorically inaccurate, it's also kind of stupid, IMO, because it confuses and obfuscates public understanding of the meanings, underlying causes, and significant differences between behaviors motivated by hatred and those motivated by fear.
However, I also realize that the current definition, however inaccurate, is already so entrenched in our cultural lexicon that this whole thing might be too little, too late. But, it doesn't hurt to try, I guess.