In San Francisco, major bus routes are notoriously unreliable. It's not at all uncommon for one to just not show up, and the next one to literally be so full they can't let any more people on. There have been some complaints about the N–Judah turning back before completing its run to the outer sunset, but light rail in the city is much more reliable overall.
As with other suburban sprawl, the valley doesn't have enough density to pull off good service. Buses are infrequent and you may have a long hike to and from the nearest stop. Caltrain is fast and very reliable (IMHO, even fewer delays than BART) if you happen to be travelling between a handful of city centers (some stations have housing nearby), though they haven't decided yet how much service to cut due to budget problems (the worst case was going to be 8–5 commuter-only).