Flying is expensive, yes, and things like skiplagging cost the airlines money and they pass along those costs to the consumer. So whoever is skiplagging could just be helping to drive up costs.
Cost is a tough thing to quantify in this case. It is more a person taking advantage of promotional fares. While I do not partake in skiplagging, nor would, you do run into inane pricing from time to time.
A good example, I live in Iowa and we planned a family vacation with adult children in the Yucatan a few years back. We found a great deal to fly from Iowa to Minneapolis to Cancun, a few hundred. My Daughter, who lives in Minneapolis tried to book the same Minneapolis-Cancun flight the same day we booked, but for her, with one fewer leg, it was twice the price. She did find a cheap ticket, similar in price to ours, but she had to fly Minneapolis to Detroit, then to Cancun. Much the same on return.
It is hard to imagine that flying fewer miles and fewer flights costs the airlines "more", it is purely market driven pricing...want a direct flight? pay for the convenience.