A lot of people think those who ask for shoes-off in their homes are 'germaphobes.' It is certainly true that a lot of people who have a shoes-off policy are parents of small children who are concerned about germs being walked in on peoples' shoes. This is a quite legitimate concern.
This concern is often countered by the so-called 'hygiene hypothesis.' This holds that allergies are currently on the rise because peoples' homes are too clean and modern children are not sufficiently exposed to bacteria. There is evidence to support this theory, even if the jury is still out.
Even assuming that the 'hygiene hypothesis' is correct, there is no obvious way to decide how much dirt is healthy. Very few parents would be happy about cooking in a dirty kitchen, or having their children sleep in filthy rooms. While some bacteria is good and healthy, some bacteria can cause all sorts of diseases.
More importantly, there are some things that your shoes pick up that are not germs, but very much in the unwanted category: lead, pesticide, weed killer, dog excrement, roundworms, dust, pollen, plant sap, mold, toxoplasmosis (a parasite which is transmitted through animal excrement and which can survive in infected soil), cigarette ash, arsenic, mecury, asbestos, cadmium and thallium.
Simply put, your shoes can pick up anything. Please keep them out of the house.