From my 30 years of experience in cooking I can say that there is nothing to worry about food safety when you are using microwave ovens for cooking or reheating. You may use a cover if you are reheating some liquid type food such as a soup or while making some pop corns. It's just for preventing over flow or scattering outside of the bowl. If you cover your food with a lid while reheating any food, you can prevent drying out of the stuff. You can retain moisture within food while using a cover. So it's upto you and the type of food you cooking in microwave, you should decide whether to cover or not.