Simple, most airlines have computers that can calculate at what cost of a ticket to a particular destination they will make the most money. This can fluctuate by time of day, what direction more people are flying and also here's the really complicated part.

The planes go on specific routes so even if they don't sell a ticket between 2 spots that plane still has to travel there to pickup the expected passengers at that destination.

It is all a factor of some routes while shorter have more demand and they can charge more.

Also interesting I once tried to book a ticket somewhere, saw that the price was say $300, but included a layover in a major airport a couple hours away. The layover was longer than it would take me to drive and the cost of car rental in major city was less. I then switched to just flying to the major airport but then they tried to route me through another hub first. I clicked non-stop and the price was $500. It is psychological, they can charge more for a "non-stop" so they do.