Your point is well taken, I hadn't considered that. It is true that there are people who would not want the money to go to AIDS research (hopefully because they think another cause deserves higher priority as opposed to having misplaced fear/hatred for people with AIDS). I don't think that this is the primary reason Apple chose to do the donations with only one color, but you never know.
It is too bad that there isn't some way to donate when purchasing another color. Yes, it's true people can donate money on their own, but look at how many people don't send in rebate forms even though they will get money (sometimes $100 or more) just because they're too lazy to do so...