The screeners have no problem distinguishing Israeli Arabs and Sephardic Jews. 30 seconds of conversation -- if not simpler cues such as clothing -- will resolve any ambiguity.
Israeli Arabs might not always be hassled, but they are certainly lined up for "increased scrutiny" more often. A lot more often. I have enough friends who can attest to this experience.
I cannot count the number of times I've flown via TLV -- let's say that I've departed a few hundred times over the course of my life. How many times have I been taken aside for any kind of additional screening?
Zero. Never. Ever. Every time I have flown, I've received the abbreviated white-jew-boy questioning about my bags and whether they've been out of my sight. That's it. Nothing about me, ever. Obviously, they deem me to be inherently safe, else it would be wise to randomly subject me to extra screening once in a while.
Without getting into the advisability or ethics of racial profiling, we do it unabashedly in Israel, and that's a fact. Unlike the US, the threat profile is relatively narrow: Arabs and/or Muslims, and the one-time Japanese freelancers. Ergo, it makes practical sense to invest the majority of your screening resources in one place.
As harmless-looking, pasty-white, computer-geek Israeli Jews, we feel the touch of the security apparatus more lightly than everybody else. Don't let that fool you into thinking that everybody has it as good as we do.