Once an aircraft leaves the ground, it runs for 'free' through the air bearing only it's own costs - not that of the air around it that supports it's very flight. Naturally, there are overflying costs and ATC costs but these are in a different league to owning and paying for every cubic inch of the air!
Eurocontrol charges are pretty steep, especially in/from the UK. They are also calculated using the square root of the aircraft weight; so Ryanair, using smaller, short-haul aircraft pay more per tonne than BA using a jumbo for long haul (for example). Not too different to the current rail situation here in the UK, where the track is owned centrally and the operating companies pay to use it.
I'm no fan of Ryanair - they are the Tesco of the airlines. Like Tesco, they have certain business practices that I do not like, so I prefer not to use them. In case of dire need I will - and know exactly what to expect. The consumer, these days, is mostly focussed on cost and MOL works this to perfection. You have to admire the man; he's a superb player.