And remember that all water must be treated. So the real question is, why is sewage different than all of the other contaminants that get in fresh water?
The standard scientific (chemical) process is the mechanical separation and dilution mentioned, but there is no evidence that there is a safe level of hormone that can be absorbed daily. Not unlike DDT: actually hormones were cited as evidence during the fight for the ban. However, there is scientific evidence of sexual mutation in creatures living in water (frogs, fish etc. -- though many other things could be blamed for this, but none rule out the above)
If a virus will find way to bypass all filters and return back to human body, then we will have huge problem.