A few years ago I flew from Israel directly to Egypt, which I will never attempt again. In the time I spent in the Israel airport before departure, and the time it took to clear Egyptian customs after coming from Israel, I could have flown to Rome, then on to Egypt on a separate ticket - which is what I have done since then. The travel agency didn’t like to book it like that, but when I told them they could come with next time, they relented. But I will say - I never felt safer.
I found flying in and out of Cairo to be time consuming and difficult. Very high security. And Israel more so? That’s impressive.