Is faction the only thing that determines factioned-NPC aggression?

[Vladesch]

Same faction, same race, different class. So it would seem the NPC's class (and I would guess race too) affect your faction standing. Interesting find.
It is well known that your own race and class will affect faction.
I suppose paladins hate either your race, deity or class more than clerics.

BTW: NPC's are only on 1 faction. The faction hits you get when you kill them are unrelated.