To make a 40 mile run in an hour, a bus needs to do very few pickup stops in SF, drive nonstop to destination, then do very few drop off stops in Silicon Valley; then return empty to repeat. Same thing other direction for the evening trip. It's the sort of trip that only makes sense for a chartered coach, not a public bus.
If the route was provided by the local muni bus, people would protest that too - that tech employees were getting special treatment, that a SF tax funded agency was serving geographic areas well outside of SF, that stops should be added at all the intermediate cities (doubling the length of the trip), the system would be more wasteful as buses would run empty on company holidays, and that the companies should directly provide those routes themselves since they only benefit them.
The system presently in place actually makes far more sense than trying to expand muni because it's a very specific purpose and specific route.
For a company with no shortage of money, a shuttle makes complete sense.
[1] https://www.google.com/maps/preview#!data=!4m17!3m13!1m1!1sM...
(EDIT: Added 3 mile source since someone below questioned it)
The issue with Caltrain is that there are simply not enough trains running on it to ferry all the people who need to get to the South Bay. My ideal solution is better express routes through the city to the caltrain station and from there shuttles to the corporate campuses. We'd need some serious infrastructure improvements to the caltrain however.
I wish companies were more willing to spend their lobbying money on pushing politicians to commit to infrastructure improvements that could benefit a broader stripe of the population then just their employees.
Being a pedestrian isn't any safer as we had a record number of car vs pedestrian deaths this year.
We are massively under served.
Sure, want to put more money into that sink, and see it wasted?