This works so well on cruise ships as hardly anyone ever gets sick on those. A tiny hole in a filter membrane is huge to bactera and viruses.
Lots of people are worried about bacteria but 99% of the bacteria on the planet doesn't like humans and is safe to consume. The bacteria that lives with humans or comes out of humans is what will kill people.
Then there are prions which will pass through these filters which is why the systems that don't concentrate diseases always have a large natural buffer that is full of creatures that mess with whatever manages to get pass the sewage treatment systems. The places that are talking about bypassing a large natural reserve is asking for trouble. A large lake or a river have plenty of life that will kill off most of the nasty things but if that cycle is short circuted, there are plenty of things that survie in fairly pure water for days or weeks.
With the cost of deslinating water, it makes more sense to use ocean water than water with too high of human waste and the health risks are far lower as well.