I'd quibble a little with that, or maybe just clarify; there are two kinds of rail systems in the Bay Area -- local (MUNI in SF, VTA in Santa Clara) and regional (Caltrain, BART, Capitol Corridor). I really think regional rail serves a purpose. For all the tomatoes we tend to throw at BART (some of which it certainly deserves), it's a big contributor to keeping cars off the road -- or letting people get by without cars -- for trips that you really couldn't walk, such as between SF and Oakland. When I worked in SF and lived in Foster City, I was taking Caltrain in daily, and while that wasn't without problems it was a hell of a lot nicer than driving -- and once you figure in not only gas prices but parking fees, cheaper.

On the local level, as much as I've generally preferred to ride trains rather than buses, I think you're right -- although buses are helped immensely by having dedicated bus lanes for main arteries, and I'm not sure how feasible that would be in SF.