I use a
Thule "Round Trip" case I picked up at REI, and really like the protection it affords. It easily accommodates my 61cm frames. I fly Southwest almost exclusively, and they charge $50 each way.
My experience has been that TSA will open the case and look through it, so I always include a photo of the packed bike inside the case so they'll know how to repack it if they decide to take the bike out of the case for some reason. So far, everything has arrived intact and undamaged, with a nice little note from the TSA that includes a phone number to call if you're unhappy with their repacking or if something is missing.