>But our animal bodies evolved to live in the dirt, no?

Evolving while existing on or tolerating dirt is not evolving -to- live in the dirt. It may very well be that some exposure to pathogens is beneficial, and some of that may be conferred by contact with animals (I know daycare does that job for sure), but I will still work to reduce my exposure to it within my home and on my body.

If I recall correctly, properly managing waste (human and otherwise) via sewage and plumbing has been a material contributor to decreased morbidity/mortality rates in the developed world.