The Pacific Surfliner (Amtrak) is a great train ride, running surfside for a fair number of miles between San Diego and Anaheim. We took this ride round trip and really enjoyed the scenery. We timed our trains so we returned as the sun set over the Pacific. If you want, you can walk a few blocks from the station in Anaheim to Disneyland, or go to an Angels game (the stadium is adjacent to the station).
As suggested above, Coronado island is definitely worth a visit. The town is walkable with a small movie theater and lots of good restaurants. The Hotel Del Coronado at the foot of main street is a huge old wooden structure right on the beach. Definitely worth walking through. We stayed there and it was very pleasant. The food is very pricey, but a drink on a terrace overlooking the ocean in the early evening isn't too expensive.
If you are up for a drive inland, Palm Springs is about 2 1/2 hours away. There is a cable car ride up a mountain that provides panoramic views of the desert. There are many shops and restaurants in Palm Springs. It is an amazing place. We drove out because we had two days of chilly foggy weather (the locals call it the "marine layer" -- we call it fog) and wanted to warm up.
You can also drive north a bit to visit La Jolla, a wealthy area with lots of high end shops and some very nice beaches.
You definitely don't want to miss Balboa Park, the Zoo and the San Diego Train Museum. The layout operators are very friendly and will invite you to see the controls if you show interest and ask some questions.
Have a great trip!
