That whole thing was bogus, they mixed expenses from the County of San Francisco with the City of San Francisco (because the boundaries are the same). Factor for that, and it's actually well run for a city with a major port, an airport, a great public transit system, and an open source policy.
Oakland handles all the container ships, SFO is in unincorporated San Mateo County, and the public transit is objectively bad - terrible compared to New York, Boston, or Chicago (and possible other cities I haven't been to).
is there any reason other than our collective stockholm syndrome not to expect a modern shipping hub and technological powerhouse city to be run at a hefty profit?
I'd say it's a good reason FOR using open source.