Their system incorporates subjectivity. How was the pass protection, was it a clutch play, was it a good throw, and a number of different variables.
The more subjectivity that is in play, the less reliable the scoring system. That's why PFF sucks. They have average Joe's rating on a subjective basis. How else could they possibly have a grade for every single player in 3 or 4 days? Anyone here care to rate a Jaguars game? Probably not, and the same goes for just about any other team that a fan doesn't follow. The consequence of this would seem to be that they have fans rating the games of their favorite team.