No, they're not really that different at all. They're both based on negative racial stereotypes. They're based on the stereotype that white guys aren't athletic enough to play CB or RB and they're based on the stereotype that black guys aren't smart enough to play QB. They're both negative, just one is physical and one is mental. That's really the only difference.
Here's where I think the difference lies...white players are often characterized as less athletic than black players. It is a negative, that is true, but compare that to black players, especially QB's. Too often, when they struggle it is attributed to a fault in their character, as opposed to what their bodies can do.
Whether it's McNabb getting blasted for a lack of courage or Cam taking heat for not acting "properly" when he is coming off a loss, it is a different kind of attack than is typical with white players. Sure, there are outliers on both sides, like character flawed Ryan Leaf or Jeff George or even Cutler, but character attacks seem to come much easier when dissecting the game of black QB's.
In Cam's case, the guy has done nothing since he joined the league to warrant the character attacks. He hasn't yelled at his coaches or the officials. He hasn't pushed one of his teammates or a cameraman. He hasn't publicly called out a teammate. He has done none of that (and all the above are real things that high profile white QB's have done). So ask yourself the question, why him? Why is he the guy that gets singled out?