I have gone through similar feelings and you raise a great point: The buses from Google, Facebook, etc. are far better than those same companies quietly doing nothing as their employees clog the freeways, which is very common among other companies but basically invisible. So they get crap for doing a good thing.

Here's the flipside, although I've never heard anyone actually make the first argument:

-Google the company actively dodges taxes, albeit through tactics common in the corporate world. So while it is pampering its own employees, it is undermining public transit by not paying nearly its fair share into the federal (and likely state) pools that help fund the transit for everyone else. Thus, Google is actively exacerbating inequality.

-Google's buses use public land intended for public transit to provide "stops" for its employees. Google can clearly afford to compensate for this, but, as far as I know, does not do so. This at a time when Muni and other transit agencies could really use the money. Free rent for large corporations is never going to be popular.

-Although there are environmental benefits to the buses, Google, Facebook, etc. are almost certainly not motivated primarily by the environmental benefits but by self interest. In other words, the freeways are full, and getting to South Bay each morning is a nightmare. And yet many desirable engineers etc prefer to live in SF vs South Bay. Hence, the buses, which make it easier for these companies to recruit. This competitive element then puts pressures on other smaller internet companies to run their own buses, even if those buses are not particularly full or if they are driving large distances within SF to pick up only a small number of people or single person at a given stop.