Everyone complains about public transport in the Bay Area, but I think that it's actually not that bad.
I'm writing this from a comfortable, WiFi enabled bus that is taking me from San Jose to Santa Cruz. I have enough space, get to see a nice view out of the window, don't have to concentrate on driving and it'll only take me an hour to get to my destination.
People often complain about the CalTrain service between San Francisco and Palo Alto. However, their usual complaint is that it's 1 hour between services, yet they forget that it's an extremely fast way of getting around and pretty damn economical. The chairs are also really large, some of them even have tables and a power outlet. I can't imagine a more pleasent way of getting around!
Good on you Bay Area public transport!