I understand your unfairness complaint. So, to answer it, I'll explain why I still use it this way:
If I were to send wave after wave of peons after the players, stockpile the earned fatepoints for the BBEG, then come into the final conflict with 10 fate points and burn them all up on a severe attack, then I would totally agree that giving the BBEG the points would be unfair.
I use the points instead as more of a pool from which to write scenes. While I can certainly just proclaim that the bad guy has put snipers on the roof, booby-trapped the door, and taken the effort to invest in kevlar underneath a fireman's coat, it helps give me a limit of how many such conditions I should give the bad guy. It also tells me that this BBEG is invested in the story (and players are probably invested in their struggle with him), when I see that he's got 6 fate points available.
Really, though, it serves as an indication of how worried the bad guy is about the players. If they've trounced 3 of his best hit squads, then heck yes he's going to add extra layers of protection.
This works pretty well for "uncovering aspects" as a bad guy, too. I mean, you know your half-fae PC is a bit sensitive to cold iron. But at what point does a DM reasonably declare that the bad guy knows this?
If you left a mook alive and he had uncovered this, he can certainly run tell daddy BBEG, who now not only knows your weakness but has a handy free tag for it.
But if you didn't make that mistake?
Any DM can declare that the bad guy researched you. But if the DM tracked that bad guy's interaction with fate points, and then marked off a fate point to roll on such a research (investigation, really) check, then you'd probably find that the DM pulls LESS of this "i know your weakness crap" than he would have previously. Because he's only given the bad guy 2 fate points, and needed them somewhere else. Like for the snipers.
So, basically, I've just become used to thinking of how the bad guys create their actions and available resources in a scene based on the game mechanics of manuevers and declarations, backed by a fate-point economy where they are earning points for their machinations.
And, to answer the question: If the players sent in, say, the local PD, and the PD wiped, then someone in the group is probably getting at least a fate point out of it. Because I'm going to make trouble with that later.