I personally don't give a rats ass on Arabs rights! Profile the hell out of ALL of them! I'll be damned if I'm going to get on a plane with my family only to die for political correctness sake! Any Arab with a weapon should be thrown off ASAP!!!! The pilot is 100% right! He has the duty for the safety of his passengers and crew first and someone rights last!
See my earlier reply about the G-U-N. Personally, I wouldn't have given a rat's patootie about the man's ethnicity. Just the fact that the guy was carrying would have put me on red alert.
And, BTW, the best argument against profiling (especially in the long-run) is what happens if the terrorists start recruiting more Jihad Johnnies, or using people who don't fit the profile. That's why the G-U-N is the BIG deal.
To my mind, that makes checking the agent out a no-brainer. Both the agent and AA should have realised this.