In theory, an airline is only allowed to operate from its own country to a non EU destination, however there are exceptions especially for charters. It just means an airline has to get permission before hand and it is usually refused by the host countries.

For example, each year there are many Canadian aircraft operating charters within the EU on behalf of charter airlines and in principal should not be allowed but a blind eye has been turned under various excuses.

Back to Ryanair, IMHO Israel is just too far anyway in terms of aircraft and crew usage and extra security etc. which is necessary to operate there.