Recently I was in Europe and noticed a lot of backpacks on the luggage carousels. A few had covers to protect the straps but most didn't. It reminded me of an unfinished project I had and that was to find an airline shipping cover to protect my ALICE large pack. I found one at REI and it works well. And it only costs $29.50.
Here's the link to the pack cover:
http://www.rei.com/product/787296/rei-pack-duffel-bag
It weighs 1 pound 5 oz and folds to 10.5" x 9" (my measurements). It's well made and the nylon is thick. Folded up it fits under the flap or in the radio pouch.
My modded ALICE large fits in it and there's room for a rolled Thermarest sleeping pad. The cover is a bit long but you could put a spare set of boots in it and some other gear if you wanted to.
You can lock the zipper to prevent theft from the "baggage handlers". I use a TSA approved combo lock.
See the attached photos.