I don't see any reason that individual Bay Area cities cannot pass laws against Waymo operating there. Why they would do so is a different matter. I'm hopeful though.

I suspect the reason is that California cities do not, in fact, have control over this aspect of regulation. I won't claim to be a policy expert, but the failed SB-915[0] seems to imply that this is the case. SB-915 was a proposed bill to allow cities to permit or regulate AVs. It seems reasonable that if a law was attempted to be passed to permit cities to regulate AVs and the bill fails even after modification that it was the case that cities were previously unable to regulate AVs and cities remain unable to regulate AVs. Absent greater knowledge on the subject, that is.

0: https://leginfo.legislature.ca.gov/faces/billNavClient.xhtml...

Municipalities are generally preempted from regulating matters of statewide concern. In CA, the state decided to have the CA DMV regulate operational safety and the CPUC regulate the commercial service. Individual cities are prevented from enacting local laws that encroach upon state authority.