Yes, reusable bags can collect bacteria. No, that doesn't mean it's back to plastic.
Denver News just ran a story about bacteria in reusable shopping bags. It turns out that if you don't wash your cloth bags, they get dirty, and collect bacteria. (Who knew!) The "study" is pretty anecdotal but, to its credit, it doesn't appear to be funded by a plastic bag company (like previous ones). However, the story is being handled pretty irresponsibly. For example, the Freakonomics link to it is titled "The Downside to Reusable Bags," which contributes to the troublesome narrative that reusable bags are as bad as or worse than single-use plastic or paper ones. That's not the case. And while there is a small environmental cost to washing your reusable bags (which you should obviously do), it's not on the same level as producing countless items of single-use plastic.