You are asking the wrong bloke. I am a former air traffic controller, I am not an accountant. Have a look here:
EUROCONTROL - Budget
As for route charges my understanding is that they are set to cover costs, they are not allowed to generate a profit. They are cheaper where facilities are more basic. This has the effect of pushing the traffic towards areas less well equipped to deal with it. Don't start me on that!
The divvy up of fees is not as you describe. I think we take 1% of route charges and distribute the rest to member states according to their rates. Things like SESAR are the subject of other contributions from member states. There are others better qualified to answer this
