San Francisco is both a city and a county, unlike San Jose. In addition, you can't directly compare municipal budgets without taking into account enterprise departments that are meant to be revenue neutral, such as airports - in this case, both have an airport.
True but if you’re talking about per capita spending, the $650M for San Jose’s airport is about a billion dollars less than SF is spending on the much larger and busier SFO, so even that really skews the budgets.