Taxes remain payable as per double tax convention between countries of residence of the employer and the employee. (eg: Pilot living in Italy working for FR in Beauvais will pay social security in France his taxes would be Italy and/or Ireland as per tax convention between those countries)
Tax conventions mention "international operations" when talking about aircraft operations, if ryanair flies between 2 airports within the same country and one or both of these airport happen to be bases (regardless of ryanair's denial) then the convention doesn't apply anymore but the national tax and labor law does.
It's coming, slowly but surely.