From a pilot's perspective, the negatives greatly outweigh the positives.
1) Since 9/11, unarmed passengers have done quite well at stopping breaches of the flight station.
2) Since 9/11, doors have been reinforced, and crews trained to not allow access to the flight station once the airplane is away from the gate. Hi-jackers aren't getting in without breaching charges.
3) Since 9/11, flight crews have a different mindset about the negative impact of letting a hijacker take control. They won't allow it.
4) Due to the nature of an airliner, way too many innocents are crammed into a very tight space; the odds of executing a clean shot (or, more likely, clean shots on multiple targets) in such a scenario are extremely poor. Odds of hitting an innocent, or damaging a control component or fuel line, or even hitting a flight crew member, will be higher than odds of hitting a legitimate target for the vast majority of CCW holders.
5) As pilot, I would not accept a flight that authorized random CCW types to carry on my plane. I'm pretty sure my friends in the industry, and this includes a lot of FFDO's, would feel the same.