I had a low battery once too because I did a lot of short trips. The car uses more power starting than it can regenerate. Also when the car is turned off, it still uses the battery for things like the GPS, the hard drive, etc. So your SA is not completely wrong.
Like CalgaryX3, I'm on my original battery but I use a trickle charger once in a while to make sure my battery doesn't go too low. I'm surprised though your dealership didn't notify you of a low battery level before it became dead. They found mine was getting low during one of the oil changes.