I had this problem with Hertz in BOS in early May. I had flown into BOS several days earlier when selling my house there. Days later, I arrived by T (the subway) at Logan to pick up my rental for my drive back to Colorado. I had "not arriving by plane" on my confirmation and a lower "total estimated amount" than when I tried it with a flight number. However I needed to have the car switched due to them giving me a Jeep Liberty (15MPG) vs. the expected Ford Escape (19MPG), given the upcoming 2200 mile drive. When they reprinted the contract for the swapped same-class vehicle, the airport concession fee appeared and both the clerk and manager claimed there was nothing they could do. When I showed them the confirmation from the reservation made in March for the May rental, they claimed "Logan airport just changed its policy and now requires it on all rentals".

I think I got scammed but since I had serious miles to go that night, I couldn't waste much time arguing about it.