I have flown a bunch of times with my bicycle, sometimes in a box, other times in a plastic bag provided by the airline.
The bicycle held up fine on every flight – except once.
By happenstance, I was a witness to the damage. While sitting in my seat in the airplane, I glanced out the window, and watched the baggage handler aggressively throw my bicycle overhead into the hold.
The main damage: one of the wheels went out of true, which necessitated a trip to a bicycle shop.
I wrote the airline to ask for compensation (about $50 for the tuneup). I also asked the airline to reprimand the baggage handler for his shoddy treatment of my bicycle. (The airline eventually sent me a cheque, but did not acknowledge that one of their employees mishandled my luggage.)