One thing you can do to protect it, it to close all the buckles, and tighten the straps (and for example roll up the ends and fasten with elastic bands). It is also a good idea to wrap the hip belt around the backpack (sort of "inside-out") and fasten it. Just to minimise stuff flapping about.
If you want to wrap it, I know plenty people who use a big heavy duty trash bag and a roll of sticky tape. Easy enough to bring a spare for the trip home.
- DanishFlyer
(who has one of those pack flight bags somewhere, but now just end up with a duffel with backpack straps - not enough walking with bags anymore …)