This is very specifically about the San Francisco city area. The peninsular and south bay are much more suburban and family friendly.

Palo Alto isn't a lot cheaper that San Francisco it has a reputation as being much more family friendly and has some good schools. Also, Mountain View, Los Altos, Sunny Vale, Santa Clara are all more affordable and family friendly than San Francisco.

Disclaimer: I'm a single guy with no kids, so what would I know?