A variety of reasons:
1) Bigger planes are more efficient per passenger in terms of fuel, and cheaper to fly in terms of crew cost (flying a 100 seater means you need to pay one pilot per 50 passengers, in a 300 seater you only have to pay one pilot per 150 passengers. Even with a relief pilot, it’d still only one 1 per 100 passengers)
2) Bigger Airports have more competition, which drives prices down
3) at bigger airports/hubs the airline often has their **own** check in/ground handling staff as well engineers/maintenance, whereas as at small/non-hub airports those things are often sub contracted, which is more expensive for the airline
4) Flying between large airports means a larger demand for carge transportation, which is a large profit driver even for passenger airplanes
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