It starts with the fees the airport authority charges for origination and transit. They don't have to charge the same amount. For example, MUC and FRA charge different airport fees. So in essence they compete with each other. Here airports can charge $4.50, no more, no less.

In a perfect world, LGA, EWR and JFK could charge different amounts and compete with each other, service for price. MUC is more expensive to transit, but most flying LH would rather transfer there than the cheaper FRA. And in most of the world, the airport authorities run security much like in SFO, subject to government-imposed standards, and pay for it with the airport fees.

Comprehensive guide to European airport taxes and fees - Points with a Crew
(This is an old document, but you get the idea).