When you fly out of Ben Gurion, all airlines use El Al security.
When you fly to Ben Gurion, you may or may not get El Al security. For example, when I flew Delta to JFK and back, we had to go through security twice at JFK – once in the normal place (before heading to the gates) and again just before walking down the jetway onto the plane. A Delta person told me “the Israelis insist that they watch everyone go through security a second time.”