It is a nice station but food service is not available in the station. There is a cafe on the Surfliner and unlike some cities (St. Paul :angry2: ) the station is located in the midst of downtown with the ability to answer most culinary whims within a mile or 2.
As it happens, I was at SAN today. I ate lunch at little place called, I think, Cafe St Tropez, which was pretty good. It's right at the San Diego Trolley stop across from the Santa Fe station where Amtrak stops.
Funny - I happened to be arriving on the Surfliner yesterday into SAN, arriving on the train slated to arrive at 12:25pm (it was delayed a bit out of LAX due to a stuck door - which us passengers transferring from the late-arriving SWC were thrilled about). I'll be there again on Sunday when I go to depart for my Sugar Bowl trip.. There is a vendor that sells snacks/coffee/etc inside the station, and there is some places to eat over at America Plaza (basically right next to the station). The SD Trolley also runs right to the station, so you can use it to get to various other places around SD if you have time.