If the root complaint is that housing prices are going up, then San Francisco and its residents are at least as much to blame as the economic success of their region. They consistently vote to nix new housing developments because they feel it will upset the character of a neighborhood, or block the view of an adjacent one. To put it bluntly, it's property owners voting down measures that would dilute their property value and current tenants voting down measures that they feel would change the demographics of their neighborhood.
The city is a popular place for young people to live, and with proximity to strong schools like Berkeley and Stanford, young professionals have money. Without growth in housing units, the free market will push housing prices up so long as demand will support it. This is just like any other real estate market in the country.
Many residents complain that the tech buses are using public bus stops. That's between the city and the tech companies, and they've got a negotiated agreement. Maybe the residents are not happy with how their city represented their interests and what they got in return, but that's between the residents and their government. As of right now, the tech companies' use of public bus stops is legal and agreed-upon. Any protests against that use should be at city hall, not at the bus stops.
As for mass transit, that's a hugely sticky issue in the area as well. Caltrain fares are more than the cost to drive for a given distance and it doesn't connect to the BART system, nor does it wrap around at San Jose / Milpitas. The state can't afford to buy the land or pay the construction crews to connect and harmonize these lines, nor will homeowners allow for significant expansion due to the perceived loss in home value. And then there's the problem of the entire western half of SF, where there is no rail or subway at all.