1) Wash you hands regularly and cough/sneeze into your sleeve.
2) Don’t take plastic, paper or reusable bags into a bathroom.
3) If someone who is sick or may be sick uses or touches your reusable bag, wash the bag in/with soap and hot water then wash your hands.
4) Wash your reusable bags periodically – especially if you see leaky meat or produce juices on/in the bag.
5) Use common sense. You don’t have to wash your bag after every use, especially if you use the precautions above. Maybe designate some of your bags for dry items that are packaged and other bags for meat, dairy, produce or other similar items. Simply mark them with a permanent pen and check on them periodically. You don't have to add extra laundry loads for your reusable bags, just toss them in with your clothes.
Time and Beth Terry both offered good perspectives on the issue and I encourage you to check them out also. And finally, an ABC affiliate titled their story about it, “If (a) Reusable Grocery Bag Makes You Sick, It's Probably Your Fault”.