This doesn't only depend to regional airlines.
Palma de Mallorca - Heathrow - Amsterdam - Heathrow - Palma de Mallorca (start 6:25am, A321, 75 min turn-around)
17.500+50.300+13.100+30.100 per day - earnings per day are 80k to 115k (full load), but you won't start with route image 100 and there will be competition. Small regional airlines in most times have no competition on their routes.
Also there are more parameter for calculating the one time fee:
- time for the slot (at night it's cheaper)
- how much slots are left at the specific time (so maybe it's cheaper to fly at 8:05am and not 7:55am)
- is the airport already served well. Is it not, then most times the fee is 0
I can understand what you say and I think small regional airlines should be supported in some ways. But, by the way, in my opinion your airline in EU2 isn't small and it's not regional.
At the end: The fees aren't a problem for small airlines, the staff salaries are (like one can read in future request and general forums).
Kind regards from Palma to the man at Bilbao with the great company building!