No, it makes sense. At first I thought it was gestapo-like, but after a while, I decided they're right.
They aren't talking about doing screening on people who charter a 6-passenger Cessna for a glacier tour in Alaska; they want to screen large tour groups that charter something like a 727 or 737, or maybe (probably) down into the larger bizjets.
So, let's say your a pilot, and your charter company gets a call from Suleiman al Hassan, wanting you to fly him and his corporate executives from NYC to LA for an important meeting. They board, you take off, and at 30,000 feet, suddenly your passengers break into the cockpit, slit your throat, and fly the plane into a building. Oops.