A direct flight from New York to Charlotte can be more expensive than a longer flight from New York to Miami that stops in Charlotte.
It only makes sense if you understand that flight distance is only one price factor. For example, airlines charge travelers more for the convenience of a direct flight, just because they can. They also charge more for less-travelled routes and routes with less competition, just because they can.
So I find it ironic that airlines are now attacking passengers that engage in skiplagging – and the websites that facilitate the practice. If they want their passengers to be “fair” with them, perhaps the airlines should behave accordingly.