Hm... I kinda go the other way around: for each major villain, they get a pool of fate points; most of the time (due to negative refresh / lack of free will) this pool starts at zero. Any time they - or their minions - are in a scene (even indirectly), compels against them (and fate point rewards from "cashing out") go to that pool of fate points. And I do use compels against them, and generally make it clear to the PCs what I'm doing. For example, if a PC uses evocation to put down a scene aspect of "Thick Fog", I'll cheerfully compel that to make the enemy gunman give up and go away since he can no longer aim at his target. (And just as cheerfully compel the same aspect to make the PCs be unable to effectively give chase.)
I don't - as InFerrumVeritas says - give NPCs bonuses "for doing what I want". I do, however, give them bonuses when an existing aspect notably complicates their plans - when pride makes them underestimate the PCs; when environmental factors cause their gunman to fail his job; that sort of thing.
That said, I'm also seriously considering adopting the Fate Core rules, where I as GM just get a few fate points per scene. It'd be a lot easier to keep track of. (Though I'd still track individual fate point pools for any important allies of the PCs - the GM pool is meant to be spent on opposition, after all.)