All I saw of the city made it seem like a giant suburb. BART stations were miles apart and therefore practically useless. It is really not that dense and traffic is not bad.
I am sure some areas are different. I was mainly in the area around SFO, and my conference was not hosted in downtown because apparently the homeless problem is bigger there, but at that level of low density and congestion, I fail to see how public transit is much of a win. People will not realistically take public transit if it doubles their travel time. And this case applies doubly to medium-sized suburbanized cities in the central US.
On the other hand, I can see what people mean about a housing problem when there are virtually no buildings taller than 3 stories except hotels in such an urban area.