It's ok to subsidise flights like Dundee - STN because in the example of that route it was done openly through a proper tender process that anyone could have taken part in.
Airports... well... that's more dodgy. Charleroi is an example of an airport that got stung offering incentives to airlines. Targu Mures is an example of a subsidised airport that's attracted attention...
Cardiff... personally I think it is on dodgy ground. There are arguments on both sides and I see the strengths of both, but personally I'd say the arguments that it's dodgy are slightly stronger than the arguments that it's not. The proximity of Bristol is what differentiates it from somewhere like Stornoway. As for Prestwick, ...