I bought a bike bag from nashbar to transport my bike whento London with me. The bike bag is flimsy, no padding or anything, so I obviously knew this wasn't the right idea, but it was cheap after all. Took my wheels off the frame, wrapped everything up in a blanket and stuffed it in the big bag. When I looked in my bag once I got it back I discovered that my break was offcenter, and though at first, actually for the entire trip, that my handlebar was bent, but it was just that I needed to slide my break back into place! This pulled on my shifter cables enough so my shifting was off the entire trip too! What a stupid mistake, and if you can get anything out of this post, it's to not make that one. Anyway, on the way back the guy at the check-in counter for my return flight offered me a safer option for my bike free of charge, so I did that and had less problems than on the way there. They shipped it with all the other oddly sized/"special" packages, might want to ask if they can do the same for you.
So my flimsy Nashbar Bike Bag worked like a charm after all.