I've used both the Coast Starlight (long distance) and Surfliner (Southern Calif commuter line) to get around California. The Coast Starlight was used to get to San Francisco and ride around there for a few days, then travel back on the train. IT takes all day to get from the Los angeles area to the Bay area, but that's about the same with an air flight (airport hassles, flight time, getting in-out of airports). You also need to expect delays; I got inot the Oakland station 1 hour late (10PM). Bicycle transport was simple roll-on at the baggage car, pick it up in Oakland. I did put a big 'OAKLAND' sign on the bike to make sure it got off there with me.
I've used the local Surfliner to get up to San Luis Obispo (its termination point) then bicycle back to the Los Angeles. Done it twice, also had some delay problems but nothing serious. This was a simple bicycle space reservation at time of ticket purchase, then roll the bike on yourself and use the on-board bike racks. East, convenient, good service, and no/low hassle.
Both trains - Great experience, lots of space, food was good and reasonably priced, and the train pricing is great, too. . If the airlines keep getting more obnoxious and keep stickin' it to passengers, I'll keep taking the train. Only problem is there is no eastbound train service from Los Angeles area - if you want to go east you have to go up to San Francisco and head east toward Chicago on the Zepher.