Seems to me that low cost carriers may not pay the airports particularly well but they bring something much more important, PAX.
PAX bring family and friends to drop off and collect them. Family friends and pax all spend money. Lo Cos dont feed their pax so they eat at the airport. Airport food is usually fairly costly. Car parking, vending concesions and the like all add to the coffers.
I think if I was running a quiet regional airport I would be more than happy to have all those walking profit opportunities passing through.