In my not-so-humble opinion, the crucial difference is grammatical.
- In "family values" or "traditional values," the word values is a noun, a time-frozen, carved-in-stone, immutable thing.
- In "San Francisco values," values is a verb. San Francisco values tolerance, diversity, freedom—as well as craziness and consumerism (witness the fuss over the recently expanded downtown Shopping Centre).
San Francisco values many things and believes in taking action on its beliefs. We call for impeachment where it is needed; we at least try to keep the military from recruiting our children. Action by the people, individually or en masse, is scary to the Karl Roves and Dick Cheneys of the world. The only values-based action they're comfortable with is de-valuing whoever disagrees with them.