SF is primarily a hub of Web-based companies - consumer applications. Though there are many big players down in Palo Alto/Mountain View. Also, startup doesn't mean only web-based startup. There are thousands of hardware and enterprise software companies down in San Jose/Santa Clara.

Here is the stack geographically, that works quite well with stack of software.

San Fran: Web based apps

Palo Alto/Mountain View/Cupertino: Web based + Desktop based software

Santa Clara: Enterprise + Desktop based software + EDA software + Hardware

San Jose: Hardware