It's not like it takes three hours, but I once heard that "just to be safe" come three hours before and that's how I schedule it. Considering that the flight is over ten hours between Israel and New York, I don't mind.
Reports are that nowadays, people spend so long getting checked that they miss their flight, so three hours are normal, or should be the expected.
Does this mean the end of flying a 40 minute shuttle flight? It does seem pretty dumb to spend a couple of hours being "patted down" and having total strangers unpack and repack your suitcase. How about just taking your stuff in a paper bag and packing after the inspection?
Or wear and buy disposable clothes?
The train is looking better, or will people just drive when possible?
Just stay at home. That's easiest!