SFO's "legitimate concerns" are that they can control activity on their property. If they want to charge rental car companies extra, that's their right. This isn't society-wide regulation, it's a business entity (one that happens to be owned by a government) deciding what to do with their own property.
A regular business could not issue the tickets SFO is issuing. A regular business would also be subject to additional antitrust and fair-business-practice constraints.
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.
