I'm not suggesting that hijackers would mug a pilot on the offchance that he was carrying a weapon, what I (and the report) are highlighting is the fact that terrorists would use any lapse in security to their advantage.
All a terrorsist organisation would need to do is find a depressed pilot whose down on his luck, and offer him a large cash payment to simply walk through security with a weapon and pass it onto one of their members in the departure lounge.
Have a look at the report (link above), as this specifically states the risks of not screening Customs, Immigration and the Police.