A few weeks ago the Israeli government signed an open-skies agreement with the EU, that will allow EU airlines to fly from any EU-airport to any airport in Israel and vice-versa.
Just found some information about this on the EU websites.This is not an effect from a membership of Israel in the EU Treaty as we have it. This agreement between the EU and Israel is kind of biliteral agreemend the EU i.e. also have signed with the US, Maroc etc. It allows EU airlines to fly from every destination in the EU to Israel and israelian airlines to fly to every destinations in the EU. But an EU airlines may not operate domestic israelian flights and israel airlines may not operate flights within the EU. So this is something different. We currently do not have the chance to simulate this agreement parallel to the current EU Treaty.