This is a great overview of the history of SF's mass transit systems, but honestly, it's really not as bad as everyone makes it out to be. Was it better when the streetcars ran everywhere? Of course. But compared to cities like Boston or Dallas or Atlanta, SF's Muni and BART are amazing, though Caltrain is admittedly the weakest link of the system.
I think the MBTA is better than Muni + BART, the percentage of proper heavy rail rapid transit is much higher in Boston (just the meh Green Line, compared to every meh Muni line).