The Solano County city of Benicia — which the Chronicle notes is still home to an unfortunate stained glass heirloom that nods to the Confederacy in the ironically named Union Hotel — is a place that is not in San Francisco.
However, New York magazine doesn't know that, or at the least they didn't put it together when they wrote the headline: "The Latest Restaurant in Trouble for Flying a Confederate Flag ... Is in San Francisco?".
Also, it isn't quite a flag, either, and it's more complicated as such. Since the "flag" appears in stained glass next to the flag of the Union in one of four stained glass windows, it's also something a bit different than, say, hoisting a flag of oppression every day. Still, that excuse might not hold up, and I don't think any of us would be surprised or upset if the glass panel in question were removed.
Further, none of this commentary is any attempt to exonerate San Francisco from complicity in past displays of terrible iconography. Take this callback to a time when SF City Hall flew a Nazi Swastika in 1935, or more appropriate to this current debate, the era pointed out by SFGate during which a confederate flag did indeed fly in San Francisco's Civic Center. But that was — holy shit, that was the '60s?