I live in San Diego. Last summer I took Amtrak up to San Louis Obispo. I forget the name of the Amtrak train but if you take the 4am train from SD to SLO you can just wheel your bike on board. It is considered a commuter line, so no boxing or other b.s. I think the bicycle car is either the first or last car. Just wheel it on board to the bicycle section and lean it against the wall. Just like on the Coaster Train. You can also pick it up in Solano Beach or Oceanside as well. SLO is the end of the line and dumps you out at about 1pm. It was easier than falling off a log.

Of course check with the station agent about the details. YMMV

ps I think I had to tell the ticket person that I was bringing a bike, don't really remember.