That's an interesting hypothesis, but at least in my experience the flights where skiplagging has been viable have always been between 2 major airports, with a flight to a third major airport as the skipped leg. Looking at some examples on skiplagged.com right now, I see flights where BWI->LAX is cheaper if you book BWI->LAX->SFO but skip the LAX->SFO leg. Same with BWI->CLT by booking BWI->CLT->NAS. But those LA to SF or Charlotte to Nassau legs aren't subsidized flights to East Podunk.
Essential Air Service flights might sometimes play a role here but from what I've seen I think the thing that creates opportunities for skiplagging is just typical airline revenue management doing it's inscrutable magic setting prices between 2 cities without any concern for the prices of the individual legs.
Essential Air Service flights might sometimes play a role here but from what I've seen I think the thing that creates opportunities for skiplagging is just typical airline revenue management doing it's inscrutable magic setting prices between 2 cities without any concern for the prices of the individual legs.