I don't think replicator technology is exactly the same as transporter technology. I think that a lot of the food items possibly operate on compressed data in order to store it. Plus, some of the recipes that the replicators base off of could be bad. Or maybe the replicators just aren't top of the line. And Federation replicators were made with healthy choices. Let's be realistic, if the food weren't healthy, everybody in the Federation would be in trouble.
Think about the problems people face this day and age, over eating and becoming obese because food is so cheap and easily available and think about what replicators can do and how that would affect society, i mean we would all be fat people in the future.