Food allergies usually manifest in hives, not diaper rash. She may just have very sensitive skin, and tomatos are acidic. My daughter had very sensitive skin when she was a baby (and still does), so anything that was acidic had to be very watered down, or she would get a horrible rash, sometimes she would even blister up! I would suggest that you have your daughter consult her child's pediatrician for recommendations on what's best to use as a barrier on her child's skin. We ended up using Aquaphor regularly, and when there was the occasion of rash, we used a prescription Questran/Aquaphor mixture that worked wonderfully.
God luck!