Interesting times!
Whether this will affect the airline's business model in the medium to long term is anybody's guess at this point.
The airline uses a number of public or semi-publicly owned airports as well as private airports.
The EC will be ruling on the Charleroi deal sometime during the next two months, and I think the outcome here will be more interesting; it's difficult to say what will happen.
My guess is that they may broadly accept the rationale behind these agreements but they may also demand complete transparency and a change in the tendering process. That might force the airline to revise its present agreements with various airports, but at the same time maintain the substance of those deals (i.e. the favourable fees and other incentives). Any 'new' rules would have to be observed in Ryanair's future dealings.
Brussels has publicly aknowledged the popularity of low-cost services, and maintained that their job is merely to ensure all those involved play by the rules.
Merely speculating though.