So, there is a practical reason why airlines dislike skiplagging. There’s a contract of carriage that goes along with every ticket, and it states that the airline has a responsibility to get a traveler from their origin to their destination. If flights get rescheduled and canceled, the airlines will reacommodate you on alternate flights from origin to destination, and are under no obligation to route you through that particular airport.
However, this is mainly a contracting provision and as long as airlines offer flights that get cheaper when you add a connection, they shouldn’t be surprised when people take advantage of it. They can ban a traveler when they do it too many times, I suppose, but Skiplagged is doing nothing wrong here.
Remember that airlines are not above gaming the rules for themselves, either. Qatar Airlines is running empty flights in Australia, on purpose, to get around restrictions on foreign airlines flying there. They have a flight to Melbourne, and also a flight to Adelaide with a “stop” in Melbourne – except they scheduled the Melbourne to Adelaide leg inconveniently, on purpose, to make sure no one would want to connect. The result is two flights to Melbourne, where normally they would only be entitled to one: onemileatatime.com/…/qatar-airways-australia-flig…
I don’t use skiplagged, but think that if the airlines want to stop people from using it, they should make their fare rules saner.