Tell apart Jews/Israeli from Arabs
Because they don't like to meet each other
This was the exact answer by a security scrutiny operator at MXP when I last traveled. Last year I was switching from BGY to MXP Terminal 1 and I noticed that there was a separate security lane for "US and Israel flights only". However: 1) no special machinery was present at those security lanes and 2) the screening area entered the same duty-free zone, and the path to the gates was common. I actually didn't see a full body scanner in MXP yet, those devices are expensive.
I kindly asked one of the guards what is the reason airports often provide separate lanes to Israel, and if extra security is present or not. That person replied like I said above. Americans don't like Arabs, Arabs don't like Jews. There is risk of a fight in the queue.
Worse, there is no separate queue at outbound passport control, so that would only be a matter of schedules.
Of course, that was the answer of an operator to a passenger. Though I want to believe them, it is possible that Israel lanes operate with extra screening but operators won't tell. Makes no sense to me. The screening should be the same for all passengers. Airport operators must make sure that no passenger is carrying weapons or offensive things.
Suppose for a second that an airport has a security lane where chances of bringing a gun in the safe zone are increased. You know what...