Grendel,
My wife always meets me in Austin and gives me a ride back to Houston - I carry the bike back myself. But the last time I looked at the transport setup, they used semi-trucks. They had some sort of rail/pully system set up where they hung the bikes by one wheel on hooks (I'm assuming they are rubber coated hooks) and pushed them back into the trailer. They had what looked like moving blankets hanging in between each bike. I have not heard any horror stories about the transport - I'm assuming it works ok. But lots of people carry their own bikes back. Personally, I'd be a nervous wreck if I didn't know exactly what was happening to my bike at all times...