We're "clean freaks" because we've learned that there are harmful microbes and parasites in the world. Millions die/have died of disease such as cholera and typhoid that are spread chiefly by poor hygiene. The parasites we don't get as a result of having clean water and sanitary sewers are on balance harmful to us.

I'm not sure I buy the "hygiene is harmful" argument or that we've gone overboard with it. I think a lot of other factors that have changed in the past 60 years might factor in, including a misguided government/agribusiness lead food pyramid that is way out of balance with our pre-civilization diets, as well as the introduction of highly processed and sweetened food that for many of us forms the majority of our diets.