I tend to agree with others that don't see why injuries to QB's would be different between college and NFL. I get that NFL defensive players are faster, bigger, and stronger, but so are the NFL offensive lines, running backs, and QBs (look how much bigger JT has gotten since his freshman year). I too thought college teams would just tee off on our QBs and knock them out all the time. That hasn't happened though. I think part of it is that our scheme lends itself to the QB usually knowing when he is going to get hit and preparing for it (as opposed to a QB being sacked from the backside) or avoiding it altogether (once the man commits and the QB decides to pitch, the QB usually doesn't continue to carry out the fake, but instead just gets out of the way), and the fact that tee'ing off on a QB without playing sound defense is a pretty easy way to let the other team take it to the house on a single play.
If the only argument is about discrepancy in athleticism (which is the only argument I think is being put forth), then, as the OP pointed out, why don't Navy's QBs get absolutely torn apart when they play the Notre Dames of the world? Why wasn't Tevin Washington torn apart by USC, FSU, etc. Is the argument that Notre Dame, USC, and FSU's defensive players are literally just to weak to hurt a college QB, but need 2-3 more years to develop? I am not sure I would agree with that.