This article is right, but also misleading. Yes, people did drink water. But they preferred to drink beer, and basically they drank beer for thirst if they could. And they did this not just in the Middle Ages, but into the 20th century.
Your blog posts doesn't discuss the medieval era at all though. You are strictly talking about modernity.
The medieval period ends around 1500 AD. A time where the vast majority of people lived in small villages. This is when population density was very low and the industrialization hasn't happened yet. Cholera is a modern problem. Water pollution is a mostly modern problem.
So yes, you are right that water safety was an huge issues in the modern era (end still is is in many regions of the world). Not sure about always preferring beer as I haven't looked deeper at the evidence but it is hell more plausible than for the medieval period.
I wrote [a blog post](https://www.garshol.priv.no/blog/433.html) that goes into this in more detail.