A few people wrote in to say that BART is what it is (mostly a commuter rail system) and it's supplemented by the MUNI, which is true, but the combination isn't quite good enough.
Not picking on SF. Transit isn't perfect in my urban hellhole either, was just pointing to the thinking behind the design of the system. An immense amount of money was spent creating a system to bring people in and out of the city, and less was devoted to moving people around within the city.