Were it not for these buses, there would be more cars on the road (and jostling for parking spots, and more pollution) and more people piling into Muni, Caltrain and BART during rush hour. These buses, like the bathrooms in Starbucks, are a private company providing a public good.
I work for a company that doesn't give me these buses. I wish they did. I'm plenty envious. But I am under no illusion that these private bus systems owe me anything more than the lightened traffic burden they already gave me.