I think if all the Google/FB/Yahoo/Ebay people who are on buses took Caltrain, people would be complaining that they were late to work because there was no space on the train.
Also, none of those places are right next to a Caltrain station so the company would have to have buses shuttling people back and forth at much worse fuel economy than shuttling them from SF.
Google does have a SF office but as mentioned in other comments, real estate in SF is not cheap and it would be a fool's errand to uproar the campus in MTV.
The problem with train and bus systems is generally that, when they have low ridership, they run less frequently, leading to lower ridership, etc. If there's never any space on the train, as long as the fares are reasonably high (which I thought they were when I commuted via Caltrain, although apparently they didn't cover costs) then Caltrain can buy more cars, more trains, and more sidings, and run every ten, eight, or six minutes, instead of about every 12 minutes during rush hour, as now. Every 12 minutes sounds good, but there are only five Baby Bullet runs at present, there are 40-plus minute gaps between them even during rush hour, and you have to get up by 8 AM to catch any of them. So if you miss your Baby Bullet by two minutes, you can easily spend an extra half-hour in transit.
So I think that more people taking Caltrain would make Caltrain more useful, not less.
Also, none of those places are right next to a Caltrain station so the company would have to have buses shuttling people back and forth at much worse fuel economy than shuttling them from SF.
Google does have a SF office but as mentioned in other comments, real estate in SF is not cheap and it would be a fool's errand to uproar the campus in MTV.