Flights can still be full but not profitable. Its all down to the yeild that they get for the seats. If they are selling the seats cheap then it will be a low yeild so they will put the aircraft onto routes where they can get a high yeild. Also has to do with airport costs, land fees etc.
Airlines are a business and the primary principle of a business is that it is there to make money for its shareholders so therefore bucket and spade routes are most profitable out of the north east so thats what is done.