Disclaimer/Disclosure: I plan to relocate to Tel Aviv soon (from Germany), the company I'm working for has its headquarter there. I like the country, try to learn the language etc.. But:
Every time I do the flight I'm nervous about the problems that _will_ come up. Coworker needed to strip to his underwear. Another one had his bag completely devastated several times. My (german, local branch) boss has probably more stamps from IL in his passport than anything else and does the trip routinely: I've never seen him getting through without problems, taking apart the hand luggage and asking lots of weird questions, sometimes for hours.
There are some procedures in place to make this easier in the future. For a while companies can now announce guests/coworkers etc. in advance and make their life easier by providing names, passport numbers and dates of arrival/departure in written form. But that takes time and sucks if you need to fly over "now".
Regarding the "safe" feeling: Nope, cannot confirm that.
In Frankfurt the normal check-in is like this:
* Check in and get your ticket
* Pass the boarding pass control
* Pass the security (think ~TSA) control
* Move to the gate and board
For El Al it's like this:
* Talk to a "Security officer" about your plans to stay and your luggage. Who packed it? Where? Did you leave it for a second? Did someone ask you to bring something to IL? etc..
* Get a ticket and a token with cryptic (probably: "Search this one, Yes/No") markers
* Pass boarding pass control
* Pass security (~TSA) control
* Go to the gate
* Pass IL security, taking that token (and, every single time I traveled) sit down and wait for an officer.
* Answer lots of questions, let them check your luggage (again)
* Move to the gate, guarded by security officers with submachine guns (remember: We're still in FFM, Germany at this point...)
In Tel Aviv, Ben Gurion, it's the same. The most upvoted post was from someone with an Israeli citizenship. Yeah - right. There are two lanes in Ben Gurion, Israeli and "Other". The latter is crap, takes ages, needs you to be there while they x-ray all your luggage (this is before you get a ticket, so you are present with your check-in luggage as well). Lots of questions. And, from experience, you end up at a desk where someone tells you to open your (check-in) luggage, to search your underwear and private possessions in front of you.
Seriously: This is _not_ better than anything you US guys are currently complaining about. And no, this does _not_ make me feel safe, at all.
Edit: Something I completely missed to mention: The article actually tries to tell you that the process is quick and effective. Maybe (not sure) it is for people with an IL passport. For me it means being at the airport 3 hours in advance, instead of 45-60 minutes. Otherwise I'm just not able to make it. My next trip is schedule to depart at ~3 am, I know that I'll be on the _german_ airport at 0:00 - for the sake of this efficient process. Same on the route back. What an improvement..