Dr. Stoopid said:
According to Leon in KH1, the heartless are afraid of the keyblade and will continue to attack its weilder. And according to Yuffie, they are able to track it down to find it's master. (Like some kind of anti - keyblade radar)
My interpretation of this is: (No real answers, just theories and opinions)
That the heartless are like parasites, feeding on the hearts of all worlds, and the keyblade is able to close these hearts, making the keybladers their enemy. It's sort of like destroying their "homes" and "food supply", which the heartless, like all animals, are willing to defend.
(And I'll go on a limb with this one...) The heartless are like slaves to the controllers of the dark arts, (people like Ansem and Org XIII) who have their own reasons for universal domination. So the heartless, to them, are mercenaries working in a mutual relationship for the side of evil in order to save themselves. A "you scratch my back, I scratch yours" situation.
Well there's my 2 cents, anyone else? (KH 2 spoiler free would be nice)