The answer depends on how you pick players. I like to do cheat sheets w/ stat projections, and then figure out how many fantasy points they would earn, and THEN add on some kind of multiplier based on likelihood of injury or poor performance or inconsistency.
The last is obviously very subjective, but for example I'd multiply a guy like Tom Brady by .97 or .98 b/c I don't want to discount him much, he's a proven performer and relatively healthy. On the other hand, a guy like Ahman Green in the RB's I might put at .86, since he's injured a ton and he has so many questions around him in GB. Vick I had at a .9, which was about as big a discount as I put on any QB. W/ that kind of system Vick comes out as the 13th or 14th best QB in my book, so a good backup.
As an earlier poster said, running QB's take more licks (and harder ones). Look at the highlight films of Vick's runs where someone takes out his legs and he does a full flip in the air, a few inches away from slamming head-first in the ground and getting concussed.