People take flights for both relatively short routes and very long routes. For example, Austin, TX to Dallas, TX is only a few hundred miles and you spend barely half an hour in the air.
So trying to decide what flights to have and how many of each flight to have is like a strategy game airlines play. If a flight is mostly empty, they either lose money or make a lot less than if it’s full. If a popular route has too few available flights, they lose money because people use other airlines.
So having a flight that goes Austin -> Dallas -> Somewhere lets them be a little more flexible than having one direct Austin -> Somewhere. Maybe Austin->Somewhere routes don’t frequently fill up, but Austin->Dallas is more likely to fill. And maybe more people fly Dallas->Somewhere overall. That means the airline makes a little more money if they DON’T have a direct flight, because they can schedule more flights closer to capacity between the three destinations.
But layovers are inconvenient and raise the probability of trouble, so some travelers want to avoid them. So for certain routes, if the airline charges a premium fee for a direct flight they can make up for the “loss” of the plane not as commonly being at capacity. From the customer side, it feels like you’re paying extra for less hassle, which is generally seen as a fair trade.
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