Imagine that they start nudging in cases where the benefit of that option isn't nearly as clear, and you have to go through that for virtually every transaction:
You reach for an item on the shelf: "Wait! Did you know you can pick this other item with slightly less fat?" Repeat x100 for every shopping trip.
Your paycheck is now 80% deductions: "We found that the optimal budget buys these necessities in bulk under these programs. Don't worry! You can opt out of this first one by going to this office, the second by going to this office, the third..."
"We found we could increase employment and reduce dependence on public assistance by randomly changing the procedure for applying for benefits!"
Source: I love Pringles. http://i.imgur.com/oibfGJA.png
The problem is a lot of reusable bags aren't easy to clean (e.g. cannot be placed in a washing machine) and people reuse bags for both uncooked meats and fresh vegetables then just leave them for long periods with food bacteria on them.
Most of the general public doesn't realise the risk, and unfortunately even if you do realise it, most re-usable bags aren't cleanable anyway. All you can do is spray them with disinfecting spray every so often and hope for the best.