The bag was contaminated because it was in the bathroom when the first person with the virus was vomiting. If you read the article, you'll see that they found the contamination on the outside of the bag, and the others were infected simply by the contact with the bag, not because they ate the food contained in it. The same thing would have happened with any type of container that had been exposed to the virus and not cleaned. The scientists have seen similar outbreaks caused by door handles and other common surfaces, but they had never been able to definitively track down a single point of infection before this case. They even state at the end that this isn't a reason to get rid of reusable bags, as it could have happened with a plastic bag just as easily.
As for the general fear of food poisoning, the bags are as safe as the person using them. If you treat them like any other reusable food container, with regular cleanings, it will be just as safe. I tend to separate all my meats into one bag, so I can wash that bag afterwards.(And that's even if the meats are also in plastic bags inside my bags to reduce any leaks) I don't worry much about the bags with boxes or canned goods.