The Valley sort of is a transit problem, more than SF. Although SF's lack of a crosstown subway doesn't help: the N-Judah streetcar plus the Geary bus, between them add up to a pretty poor crosstown transit situation. But the Valley explicitly opted out of BART and used the money to build county expressways instead (San Tomas, etc.), which is one of several reasons that it's a sprawling mess.

NIMBY-ism is also a problem in the few places of the Valley that do have decent transport, though I think it's the secondary problem. One place it's noticeable is Palo Alto: why isn't there high density housing near the Palo Alto Caltrain station (which is also conveniently near Stanford and a number of tech companies)? Because Palo Alto homeowners don't want anyone with less than a $1m house to live there. However afaik this is a minority situation in the Valley, and most of it just doesn't have decent transit that could attract high-density housing in the first place. San Jose has also been more development-friendly, although it's too bad there that the VTA light rail is so near-useless, or that area could plausibly have a more urban feel.