I've checked bikes on Amtrak as checked baggage before (in the Amtrak bike boxes) and it has worked out well. It is inexpensive (I think $20) and the boxes are easy to pack because they are so big, and the bike is right there when you get off the train and easy to assemble.
We are going to San Diego next month and we might want to bring our bikes with rather than rent. But we are not taking the train, instead we are flying (and not via Southwest), so the charge would be quite high to ship our bikes as baggage on the airline.
FedEx quoted me a rate of around $100 each way to ship a bike from our home in Minnesota to San Diego. Not bad and I already have a home made box.
But today I called Amtrak Express to see what their charge would be from Minneapolis to San Diego (both cities have checked baggage service). The agent told me it was a flat rate of $67. Very reasonable and you can use their huge boxes! So this is a good alternative to airline baggage fees IF the origin and the destination have checked baggage service with Amtrak. Unfortunately the number of cities that have checked baggage service with Amtrak is fairly small, around 100 or so according to Amtrak's website. You can buy the boxes from Amtrak, I think they are $15, but sometimes they have used ones lying around and don't charge for them at the station.
Anyway, I thought this might be of interest.