Niners Nation explains the pick:
Of all the quarterbacks in this draft, Colin Kaepernick intrigues me the most with his combination of skills and upside. I spoke with one draft analyst who views Kaepernick as a slightly taller version of Aaron Rodgers. He has a combination of scrambling ability and arm that could make him the perfect match for the 49ers offense.
Because of the lockout, the 49ers will probably have to roll with Alex Smith in 2011 but from there they need someone for the future. That appears to Kaepernick. He's been rising lately and has a real shot to be successful especially working with Jim Harbaugh.
For the full explanation of the pick, check out Mocking The Draft.