I don't think that you've got any real choice. It's not certain airports which are inexpensive, it's certain airlines. (Or, more accurately, it's certain flights with certain airlines).
If you're trying to keep the cost down, I assume that you want to avoid 'full-fare' carriers. Unfortunately, very few budget airlines serve Minneapolis. (It doesn't appear in the destination lists of SouthWest, JetBlue, ATA, Spirit, USA3000 or Allegiant). AirTran serve Minneapolis but they don't have routes to the San Francisco area.
The
only budget carrier which serves the route you require is MidWest. They fly from Minneapolis to San Francisco:
http://www.midwestairlines.com/MAWeb/
(Unfortunately, MidWest's prices seem much higher on this route than on most of their other routes. This is probably due to the lack of competition).
Chris