But your argument as to why has little to do with the actual reasons to two public transportation systems differ and you make assumptions about the history of California that are flatly just wrong. Not to mention ignore the differences in geography. California has a certain flavor of liberal politics but remember that this is recent and has not always been so, and to this day varies quite a bit depending where you are in the state. Hell, it varies depending on where you are in the bay area...
During the time New York was building some of it's latter public transportation infrastructure, my father and his brother, as teenagers, were wandering around what is now Xerox Parc and surrounding tech campuses and what would become 280 with their 30-06 rifles shooting anything they pleased. No one cared because there was no one around. It was just unused hill country. Much of the explosion of building in the Bay Area has been recent and during a period that no one wanted public transportation, they wanted a car. New York built up much of it's rail infrastructure before the car became commonplace and people really wanted to use it.
Consider this: how late in the history of New York were those grand stations built? Compare that to how far in to San Francisco's history they are building the Transbay Transit Center...
