At least they utilize mass transit. You, in your car, do not. Cars are an inefficient burden on the city and the economy. Would you rather the entire company drove?
Those aren't the two possible outcomes. The third outcome is that without the buses, the employees choose to live closer to work, not in the city. I don't had an opinion on whether that's a better or worse outcome.
There are so many different reasons that people might (at this exact moment) live 50 miles from their job. To simply say "move closer" ignores so many of them.
It's very clear that many more Peninsula tech workers have chosen to live in the city after the advent of private shuttle buses. It doesn't explain all of them (for example, some dual-career couples have one person in the Peninsula and one in the East Bay -- SF is a good point in between), but it certainly enables many of them.
The fact that so many people opt for a 90-minute commute because they think it will make their social life more interesting is much more burdensome than whether they make that commute in a car or a bus. If you want to rail against someone for something, rail against that.
I don't necessarily have any problem with people doing that myself (long commutes or driving themselves). I just repeatedly see this bizarre cognitive dissonance in the Bay Area where some of the people who spend 3 hours a day riding a bus up and down the peninsula try and assert some sort of moral high ground over the people who choose to have a reasonable commute but drive themselves, because cars.
Because cars, and suburbia. Suburbia is inherently less efficient than cities (where resources are shared). So yes, there is moral high ground.
When the south bay can compete with the cities amenities, then we will see those who value those amenities move south. Until then, the problem will perpetuate.