We were going to take the train there and back, but on the day of our cruise there is work being done on the track, and our trip would have 20 minutes on the train and then we would be loaded in busses to finish the trip (another 1 hour+). If I'm going to be subject to traffic to get there, I'd just as soon drive, so that's what we're doing.
We took the train from San Diego back to Orange county when we did our last Panama Canal cruise (Holland America). The train station is about 2 blocks from the terminal, easy walk.