Pretty simple really.
Ryanair pay or are not allowed into Italian airspace in the future.
Not as simple. Let's think like MOL for a second and suppose FR is banned from flying in Italy for these reasons.
FR has a lot of destinations in Italy, including ten bases (hubs). Some of those have FR as the only carrier which connects them to other places outside of Italy. In other cases, FR probably puts them on the major airline maps. Banning FR would probably mean all of those bases will close. If the government cannot enforce FR to compensate all the pax affected when the airline is banned from Italy, it will be responsible for those that have lost jobs in Italy due to FR departing, plus the lost revenue, connections etc. from those cities that used to be served, especially the bases.
Whether that is a big thing or not remains to be seen (can only discuss in hypotheticals), but I'm prepared to wager that is what MOL is thinking if he is thinking not to pay up the Italian fine.
The counter to all of this is that Italy does regulate its airports and routes to a fair degree to ensure local airlines have a chance (so much so that FR has appealed/is appealing to the EU that this practice is anti-competitive). Also on top of this, the Italians could bring the matter to the EU or an international court to force FR to pay up the money. It will be mostly a pointless victory for the Italians by the time they actually get the money if it goes down this route, not to mention this may provide impetus for FR to cut its Italian services in retaliation anyway.
FR has a good history of "white collar blackmail" (except "legal", of course) and extortion to survive. It will argue with airports, authorities and countries alike. I would not be surprised to see them do the same in this situation.
