One time I took public transit from SFO all the way to Monterey. I took the shuttle bus to the Millbrae station (this was before BART arrived), Caltrain to San Jose, and the Amtrak bus to Monterey. Grand total was around $15.
Just going to SJC, compared to $35 (plus tip?
) for a shuttle that may get stuck in traffic, and make as many stops as they feel like, I must say the train is the clear winner.