Here are three frequently voiced objections:
1) If the city decided to put a new bus route outside of your house, with a bus every 10 minutes for the morning and evening rush hours, then you would expect there to be public meetings where people can voice concerns about the routing, increase in large traffic, noise, and so on. Why should private companies not be subject to the same sort of democratic decision making on how to use the local public roads and bus stops?
2) Some people moved to the city in part because of the knowledge that the private bus system would be there. Without those buses, they would have chosen somewhere else precisely because the lack of parking would have made the commute impossible. It's hard then to say that each bus replaces a dozen cars, when those people might not be there if there were no buses.
3) If getting cars off the road and reclaiming commuting time were paramount, then why not rezone the areas around Mountain View, Cupertino, etc. for medium density housing, like SF-style row houses, instead of the current preference for suburban detached housing? Then people could walk or bike to work in a matter of minutes. The densities for SF, MV, and C are 17K, 6K, and 5K/sq mile respectively, so there's plenty of opportunity for local population growth. Instead, the local (and democratic) resistance to zoning change in those smaller cities causes increased prices and bus traffic elsewhere, but the people in SF have no way to push back and cause the zoning laws of the smaller cities to change.