If I had to guess the airport doesn’t make money just off of the flights, they also provide general services to passengers. Having a 30 person flight come through might net them parking, drinks, duty free revenue as well. Even some of the aero revenue like fuel or jet bridge usage are dependent on the number of flights.

Given that, the price for how much you charge an airline should take into account how many additional passengers they will bring through their doors. There has to be a price for lower frequency/more spikey carriers, but it is probably a good bit higher and could mean it is better to just run more flights.