No, the fuel is paid for because the flight is paid for. The plane is still going to its final destination, it’s just going to use less fuel because there’s one fewer passenger. I’d argue as well that skiplaggers don’t check bags, so the fuel savings are even greater since that’s one less bag than planned on both flights.
Over time, those fuel savings do add up. Airlines do care about that, or checking bags wouldn’t be an optional extra charge with so many of them. It’s just not as optimal as having someone pay the full price for a ticket to destination 1, and full price for destination 2.
Frankly, I feel that airlines can shut up. Overbooking flights is the same practice in reverse - they deoptimise passenger travel plans by bumping people when everyone who booked a seat shows up.