Trains are very different. You carry your own baggage on board, but you can carry larger bags. They do have some trains with baggage cars, but a lot of the trains are designed to be commuter trains from San Diego to LA. Can't imagine that commute personally, but hey, there are people that actually do that.
For those considering this option, please do look closer. It's a wonderful trip on the train from San Diego to Anaheim. The Anaheim station is in the parking lot of Angel Stadium, just a few minutes from
Disneyland. It's a very easy and hassle free way to get to Disneyland from the San Diego cruise terminal. The views along the coast are amazing.