I do think a lot of people undervalue QB's who play on teams that value running the football. I wouldn't blame it on fantasy - just a general impatience among fans.
"Yeah, it's great that Brady wins SB's, but his numbers don't look like Manning's."
Since his numbers started looking more like Manning's, he hasn't won a SB.
"Yeah, it's great that we win SB's with Big Ben, but his numbers don't look like Manning's."
Since they started relying more on his passing, he hasn't won a SB.
Again, though, I think it's more about coaches growing impatient than fantasy. It's difficult to convince yourself that you should "waste" time running the ball when you have a QB who can light up a scoreboard.