This study, published in Occupational & Environmental Medicine this month and covered widely, found that kids with bleach-cleaned homes and schools were sick significantly more often than kids who spent the majority of time in places that weren't cleaned so harshly.
The researchers did not point to causation but the finding reminds me of the "hygeine hypothesis." This theory claimed that the reason immune systems are going awry in modern times (i.e. the increase in allergies, autoimmune diseases, etc.) is because they are "under-challenged" due to our overly sanitary environments.
Perhaps bleach, by killing nearly every microscopic immune challenger, is causing poorly developed immune systems? Ones that are more susceptible to flu and tonsillitis?
More research is obviously needed, but I for one would be willing to stop bleaching the toilets if it meant even one less flu passed kid to kid next fall.