So if you're suggesting the airport be privatized, and then offering services like any other "business entity… deciding what to do with its own property", I think that'd be a great plan.
But SFO is a public entity, using state power to enforce extra monopoly privileges. It doesn't get to just say "because we want to do it this way with 'our' property", even if it's silly. It's the city of San Francisco's property, and their actions should be serving the public interest.
An equitable regime of charging based on actual visit impact achieves that. On the other hand, enforcing the old formulas out of tradition is lazy and destructive - and suspiciously protective of SFO's longtime partners among the incumbent rental agencies.
We still have state owned toll roads across the country. There is an established habit of limiting road traffic via tolling even on public roads.
Toll roads (state owned or private) charge by use, which is fairly reasonable and efficient, not by a deep inspection of your gross revenues.