Here is the Tokyo subway map. A colorful web over the city.
Here is the San Francisco subway. A colorful well, rainbow, that only goes down a single street in San Francisco. (It's called BART). To be fair, BART is really a bay area system meant to connect cities together and was never supposed to be much of an intercity system. But what makes up for a lack of subway?
MUNI is SF's bus and rail system. All of these routes move slowly at the speed of traffic and they break down fairly often. The only exception is where the MUNI runs underground DOWN THE SAME SINGLE STREET AS THE SUBWAY. The city collects $1.5 to ride the MUNI and spends all of it just keeping track of the loose cash.
Some people think it is too scary to imagine charming San Francisco getting a legit public transportation overhaul. But if we're serious about the green movement and uncloging the cars from the city, the eventual solution will have to do better than busses riding in traffic.