[KirillPanov]

Lack of well-protected harbors north of the Bay Area.

As you move North the winter storms get more and more fierce. You have to go pretty far inland (Portland or Puget Sound) to reach calm waters and a low enough wind speed to hold down construction costs for tall buildings.

The closest thing to an exception is Grays Harbor, which is topographically equivalent to the SF Bay but extremely shallow -- much too shallow for container ships. They have to dredge it every few years just to get the ag/lumber/automobile ships into the port.