Same with the LA area here. "Santa Monica" is mentioned once, but if you aggregated all the locations that fall into the Greater LA area, I bet it would rank higher.
Cambridge and Boston should be together, but Silicon Valley and SF shouldn't. I could walk to Cambridge from my house in the city of Boston. There is no way I could walk to Palo Alto from SF.
I have to question if you've ever done a SF -> Silicon Valley commute. There's always traffic, and the Caltrain station is inconveniently located for most of the city, which means you need to tack on time to get there. Additionally, most SV offices aren't that convenient at the other end.
There are 891 (out of 19409 with known location) job post from Cambridge, MA or Boston, MA. Which gives 4.59%.