A staggering number of people don't have access to clean drinking water and flushing toilets in the world, I refuse to start worrying about this sort of stuff so I won't be reading this article.
It's not meant to be something to scare you; the intent is to get people interested in helping with data collection efforts. It's very possible the results turns out to be that most of these organisms are beneficial to us in some way, but we just don't know without the data.
Do you also forego eating because a staggering number of people in the world don't have access to food? It's at least worth considering what it's in your showerhead since it could potentially cause a weird disease or something of the sort.
Or, as the article points out, benefit your immune system by leaving yourself exposed to what's in there.