We know that the treatment process doesn't remove everything (witness the taste of tap water in various cities).
Purification rates are generally stated as percentages, suggesting that the dirtier the input, the dirtier the output (GIGO)
Searching for "waste water treatment effectiveness" yields interesting articles about failures - for instance: http://www.cabq.gov/progress/public-infrastructure/dcc-18/in... which indicates that upstream failures treating the waste water increase health risks and treatment costs of water users downstream - why should it matter without the GIGO principle above?
How sure are you that the treatment systems remove 100% of the micro-organisms? 100% of the chemical hazards? All the time?
There's definitely room for concern, even on the purely scientific/engineering side, though advocates say that the treated waste water is the cleaner water source.