First, let us just note that this is not a system that is carefully and strictly balanced to save the game from antagonism between players and GM. If the GM is the sort to run that way, the system is not going to play well. These are more like guardrails to keep the otherwise well-meaning GM from accidentally wandering too far afield.The structure of this gives the GM an advantage - gets points for hostile invokes but has no need to pay for compels. How does it work out in play? Does the numerical advantage the players have (ie there are more of them) outweigh the GM's structural advantage?
From there, unless they've tricked out their characters to the nines (and thus having only 1 Refresh), the PCs will generally have a numerical advantage, especially considering that they only have to spend their points on themselves, while the GM has to spend them on all the NPCs. If there are 4 PCs, and the starting scene has, say, four nameless and one supporting NPC - we are probably talking about 2 fate points per PC, and less than one fate point per NPC.
If they don't have numerical advantage, that means they have bought other mechanical advantages with their refresh, and it comes out in the wash. And, while the GM is refreshing each scene, the PCs are generating new Fate points, and the GM is strongly advised to find some Compel for any PC who has only one fate point left....
And finally, there is this: When I run the system, I generally play it the following way:
In a scene in which the primary issues are not direct Conflicts with an NPC, the fate points for Compels come from the "infinite pool". But, if the PCs are in a Conflict with one or more NPCs, you may be taking some of the Compels from the NPC pool as well. If your roles were reversed, and that you are doing looks rather like a "hostile invoke" that the players might make against you, then you are apt to find it natural to take it from the NPC pool, rather than the Infinite Pool.