Just trying to sort a few things out .. El-Al, unfortunaly, needs that extra security every day. I fly to Tel-Aviv at least 4-5 times every year from the day I was born and I am quite aware of the security that El-Al and Ben-Gurion Airport has and needs.
El-Al and Israeli gouverment pays for all this high security measures they took, El-Al being a state company. I am sure that if you ask every single passanger on El-Al flights, they are happy that they're paying for extra security and are not disturbed by the checks made at the airport and check-in. Every israeli understand the need of this level of security. Even that to a european might seem a little bit to much, most of the measures taken are necessary due to terrorist attacks. El-Al did not have any security incidents from day one and that's exactly why they are taking this measures. Israel is, unfortunaly, under permanent threat from different terrorist grups. Again, unfortunaly, lately this has spreaded to EU and US too, and as you can see every civilized state as US, EU or Israel are trying to prevent such incidents. Such measures are starting to be used in european airports as well, not talking about US who already implemented such measures.
There is no political issue between Turkey and Israel, citizens of both countries are traveling free between these countries. To give you another example of free travel, in Sharm-el-sheik is loaded with israelies every year, even that relations between Egypt and Israel haven't been always perfect.
Seems nothing can stop us to travel, huh?