Note how many of the larger technology and biotech companies are now bussing a very sizable number of their employees in from San Francisco -- Apple, Genentech, Google, etc.
Smaller companies in the field are also buying into these shuttle services, eg, Genentech shares their shuttles with some smaller biotech/drug companies.
The Silicon Valley suburbs are a very unfortunate accident of available land and timing. Personally, the very first thing I did when I moved to Sunnyvale was start looking for an apartment in San Francisco -- I thought I could handle it, but found that I couldn't stand living in the area's suburbs.