It seems to me that every year when the draft rolls around their is a stigma about the quarterbacks that play for lesser teams. The perceived "fear" is that they will not be able to play up to the NFL competition, that the speed of the game would be too much for them.
I'm gonna flip the script a little bit. First, let's look some of the top QB's right now (not in any order) and where they played college ball at.
Ben Roethlisburger-Miami of Ohio
Eli Manning-Ole Miss
and some of the rising stars at the position
Ryan Tannehill-Texas A&M
It's hard to make an argument that any of these guys played for great football teams, and if the team was great it was mainly because of the play of the quarterback. When is the last time we talked about a "great quarterback prospect" from Alabama, Oregon, USC, Ohio State, etc.? Or when is the last time a quarterback from one of these schools lived up to expectation?
To me, the reason these smaller school quarterbacks are prospering is because the lack of elite talent around them. Whether it be a subpar o-line, a lack of an athletic backfield or receiving core, and non-athletic defense, or a combination of these. This means that the quarterbacks have to be very accurate with their short and intermediate passing game because they probably won't have time to throw the deep ball and the receivers they are throwing to probably aren't getting a lot of separation. They also have to have some pocket presence because they won't get a ton of time to throw from a preferred spot in the pocket. And they will have to develop the ability to read a defense and go through his progressions because he probably lacks an elite receiver who can consistently get open or make plays. This puts a lot of pressure on the quarterback, and pressure can either break pipes or make diamonds. If the quarterback can live up to the pressure, he becomes a good leader and motivator, someone the team can rally around.
With the bigger teams, the quarterbacks are surrounded with elite talent on the o-line, the skill positions, and/or the defense. This allows the quarterback to throw from a clean pocket to receivers that are probably the first or second read and are probably running pretty open so the ball doesn't have to be as accurate. And when these quarterbacks are drafted early, they are drafted to bad teams. Teams that that in terms of the NFL resemble the teams that the Purdue's, Baylor's, Ole Miss's, etc. When these top tier team college QB's get to the situation, there is a lot of pressure on them and they aren't used to losing. They aren't used to the expectation and hope that rests solely on their shoulder and they crumble.
Now, for those that are now saying to yourself, "Josh Freeman came from Kansas State, a small school". Yes, he definitely did. And at Kansas State he posted seasons of 7-4, 5-6, and 5-6. He posted a good season statistically in 2008, but it didn't translate to wins. The thing that enamored everyone towards Freeman was his "potential". He had the prototype skillset, but his biggest deficiency was his ability to read defenses. That is a pretty big deficiency, like drafting a receiver that can't catch (hi, Micheal Clayton...) Freeman has just enough of everything to give a lot of hope, but lacks an extreme amount of one or the other to become successful. He has a cannon arm, but lacks the quarterback savvy to look off safeties or fit the ball in a tight window with consistency. He has mobility, but lacks the elite athleticism to somewhat mask his lack of throwing prowess (hello Mike Vick and Cam Newton)
So when it comes to the guys like Geno Smith and Mike Glennon, the fact that they play for lesser teams and are still staying competitive bodes well for their NFL future.