Evaluating college QBs is probably the hardest task a pro GM faces. Get it right, eg Tom Brady, and your franchise is set for a long time. Get it wrong, and you have some variation of an RG III, JaMarcus Russell or Tim Couch debacle. The list of disasters is a lot longer than the successes.
I have to think a large part of it is the coaching these guys get when they get to the pros, plus the team around them. If Peyton Manning is getting pressure in his face and getting clobbered on every play and playing from behind, he is going to look ordinary.
Owners in particular are often swayed by flashy athletic skills in a college guy, see RG III. Those are nice to have, but many of the great QBs were pretty ordinary athletes, eg Brady and Manning. The really good guys all tend to process what is unfolding very quickly and intuitively. They don't have to think about who is going to be open. Then they are quick getting rid of the ball.
A big arm is a great thing, and the really elite guys have it, but you can be very successful with an average arm if you are quick with the ball and accurate. And you don't throw it to the other team.