I don't follow college but it seems like it's more about a lack of actual QB teaching than anything. Like they'll take this athletic guy who can throw it halfway decent and make him the signal caller and it mostly works because it's college. So no focus on fundamentals, little to no advancement on actual QB play. Drop back, one, maybe two progression reads, and either throw or run. And then these guys have success that most likely is only partly because of them, and NFL teams that need a QB feel pressure to go after them. And most of teams convince themselves that they can coach these guys up to the NFL level.
It never works. The guys who have success were already good QBs who had the fundamentals down and just needed time to adjust to the game. In some cases the curve is lower (see: Luck) but others need time to learn (see: Rodgers). Some can fake it (see: Eli) but far too many can't even do that. And then because they never really got coached up in College, they just fail. Those that don't are so few and far between than it's a wonder teams even bother to try.