Is it legal to fly under the Golden Gate Bridge?
No, it would violate regulations unless it was to meet the needs of an emergency.

Don't forget the catch-all regulation about reckless operation; many regulations may be interpreted very subjectively, and I feel that it is safe to say that flying under the Golden Gate bridge would attract a lot of negative publicity and would ultimately be considered something that the pilot of a fixed-wing aircraft would certainly be reprimanded for.

That's not even considering whether the bridge is 500 feet high, boats that may or may not be passing under the bridge, and your question completely truncated the 91.119(b) that lists information for congested areas, which I am almost certain the Golden Gate bridge would be subjectively qualified as.