While 99% here don't want to admit it...in college Tebow got it done, and Peyton did not get over the hump in his big games (most notably vs. Florida).
Whether it was coaching, offensive scheme, or whatever Tebow did one thing very very very well while at Florida - win. Peyton did one thing very very very well at UT - put up stats. Tebow's career and Manning's career never intersected, and the college game changed a lot from Manning's time to Tebow's time.
At the end of the day, although no one wants to hear this, Tebow was the better COLLEGE quarterback. is run and pass versatility made it difficult for offenses to plan. He was good. He earned everything he has received for his college career. However, a lot of people voted based upon the sum of their total careers and Peyton has clearly has the better football career. That's what makes polls like this tough, as the skills to be elite in college don't always transfer to the pro level.
I understand Paul's point. In college, Tebow was extremely effective as he could run or pass well enough to beat most of the defenses he played. In the NFL they took away his run ability and exposed his poor passing game. Most college teams couldn't do that.
Same reason Michael Sam was a dominate defensive player at Missouri, but then couldn't make a roster in the NFL. Success in college doesn't always translate to NFL success.