There IS a difference between national governments pumping money into eternally loss making airlines and local authorities attracting successful airlines to their locality which may,at least,create jobs and,in some cases,massively increase tourism to the area.
In one case, taxpayer money flows from a central government to prop up legacy carriers, in order to maintain employment/tourism/national pride.
In the other case, taxpayer money flows from regional governments to regional airports to subsidise low-cost carriers coming in order to create employment/tourism.
I can't see any "fundamental", or moral difference.