This is kind of an intrinsic problem with transport that needs infrastructure along the whole route (i.e. trains and cars). You need a minimum amount of travel along a route for it to be worth it to construct and maintain that infrastructure. The system naturally evolves to a hub-and-spoke model.
Planes just need infrastructure at both ends, so it's a lot easier to create a point-to-point model.
Planes just need infrastructure at both ends, so it's a lot easier to create a point-to-point model.