One of our supervisors is an avid cyclist so I will ask him. And d'oh, I suppose I could've asked him the original question also!!!
Re what's best....the ramp handling the bag (or bike) is only half of it. Obviously it wouldn't go down the traditional bag belt but realize if it does, there are things called "kickers" that basically kick the bag onto the correct belt. The force of these things is pretty strong. When the item is on the aircraft, there is shifting. While, granted, a plastic bag might make someone think twice before heaving it onto the plane or back onto the baggage cart, you will sometimes have people who simply don't care. It always makes me laugh when I see boxes marked as "fragile" because the people can take all the care in the world but once it gets on a plane with things piled on it, things are all different.
So I guess in a perfect world a plastic bag wouldn't be bad but if there were any errors at all, the bike could be damaged. Not to mention that if it is a Nice Bike, the possibility of theft always comes up. If you have anything too valuable, it isn't such a good idea to advertise the fact.
Keep in mind this is worst case scenario and not the norm. They would be things I'd think about though!!!
I'll keep my eye out in the bagwell as I walk through and see how the airlines are stacking up things like that in the baggage carts. I have to say I've never seen a bike in a plastic bag but I've seen a lot of cardboard boxes and hardsided cases.