I don't think you were rude at all. And she had no right to yell at you (I agree with the people who suspect she was having a bad day for some reason).
That being said, I don't like people eating in areas that are not meant for eating, especially in a store. I'm sure that you are conscientious and responsible enough to ensure that your child won't mess up merchandise or leave food around, but not everyone is. If my kids need to eat on a trip to the store, we eat in the car or in the cafe/restaurant seating area.