I think a lot of people aren't familiar with Kaepernick's career - he was good enough as a baseball player to be drafted out of high school but wanted to play football and Nevada was the only college that would give him a football scholarship (although lots would have given him baseball scholarships).
Here are some notes (from Wikipedia) about his college numbers - pretty impressive
On November 26, 2010, Kaepernick led his team to a 3431 overtime victory against the previously undefeated Boise State Broncos, snapping a 24 game win streak that had dated back to the 2008 Poinsettia Bowl. This game was played on Nevada's senior night, the final home game for Kaepernick and fellow notable senior running back Vai Taua. Nevada Head Coach Chris Ault would later call this game the "most important win in program history." During this game, Kaepernick surpassed 1,000 rushing yards for this season, becoming the first player in NCAA history to have over 2,000 yards passing and 1,000 yards rushing for 3 consecutive seasons. Along with Taua's 131 yards rushing in the game, the duo became the NCAA's all time leaders in rushing yards by teammates (8,285) passing the legendary SMU "Pony Express" duo of Eric Dickerson and Craig James (8,193).[7]
On December 4 against Louisiana Tech University, Kaepernick joined Florida's Tim Tebow as the second quarterback in FBS history to throw for 20 touchdowns and run for 20 in the same season. Later that same evening, Auburn's Cam Newton joined Tebow and Kaepernick as the third. Kaepernick's three rushing touchdowns in that game also placed in him in a tie with former Nebraska QB and Heisman Trophy winner Eric Crouch for most rushing TD's in NCAA history by a quarterback with 59 in his career. Nevada claimed a share of the WAC title after defeating Louisiana Tech.
Kaepernick is the only quarterback in the history of Division I FBS college football to have passed for over 10,000 yards and rushed for over 4,000 yards in a collegiate career. Kaepernick is also the only Division 1 FBS QB to have passed for over 2,000 yards and rushed for over 1,000 yards in a single season three times in a career (consecutively).