I don't know that I'm arguing that zero remnants of a "black quarterback" stereotype remain in the NFL, but I think rideaducati is closer to the mark in that NFL teams value success above all else.
The NFL is down the supply-chain from college. Athletic quarterbacks can have, and have had great success in college offenses, to the point where college QBs are selected for those attributes. So, a great many of black college QBs are athletic, and have more athletic instincts than a slower, less-agile white quarterback would.
The NFL, on the other hand, has seen far, far less success with QBs of any color who run frequently than it has seen with pocket statues. An NFL franchise MUST play the percentages or fall behind franchises that do, hence the trends at RB or WR away from white athletes. Further, the NFL has seen several extremely high profile cases of athletic black (and white in the case of Manziel) quarterbacks who were supposed to be the franchise-making exceptions but instead doomed their franchises to failure over a decade. Vick, RGIII, Manziel. Even Kaepernick could be considered as a QB who wasn't viable once the threat of rushing is removed. Russell Wilson is the only QB I can think of of any color who possesses enough athleticism to be a game changer but who can turn off those running instincts like a switch when the game plan calls for it and operate from the pocket exclusively.
There is, therefore, a strong and appropriate bias against QBs with anything approaching significant athletic instincts, and that is what would be at play with Boykin. If that is what the majority of college black QBs possess, then the NFL isn't biased from some nefarious belief, it is just reacting to the pool of candidates which are available. I would argue that college isn't biased either, like the NFL it is selecting for the attributes which make a successful team at its own level.
Jamarcus Russell, Daunte Culpepper, and Donovan McNabb were all highly-selected black QBs, and although McNabb could scoot, all three had pocket-passer instincts and that is why they were selected highly. The NFL didn't care about their color, it cared about whether they could pass from the pocket.
Now, if someone more familiar with college ball than I am knows of numerous examples of lights-out black college passers, who were successful without heavy reliance on athleticism, who were ignored by the NFL, then THAT would be evidence of a bias based on something other than NFL critical success factors. For all I know those examples are out there. But the arguments in this thread for racial bias ignore that a bias against running QBs would look precisely the same and have nothing to do with racism in the NFL.