On the other hand replacing private cars with corporate shuttle busses probably reduces general road congestion which also costs the city money.
SF is supposed to be a transit-first city. The goal is to make public transit an attractive-enough option to persuade people to use it rather than private autos. Therefore, anything that hinders public transit is bad.
The congestion in SF would also be less if those who worked in Mountain View also lived in Mountain View (or at least within a 10-mile radius).