Hygiene hypothesis posits that hygienic conditions create more immune disorders such as allergies, while exposure to allergens (pathogens) might be better to manage our immune responses. I think it is a beautiful hypothesis, but is mostly criticised.
I like the hypothesis as well, but the whole picture is very complicated and poorly understood. The Wikipedia article on the hygiene hypothesis gives a pretty good story about the various related ideas. I think most of us in related fields like and think the hypothesis is at least a partial explanation of the increase in allergies. It may be a part of the increase in a variety of diseases, including some of the autoimmune type diseases. The complete picture is complicated, but bacteria, fungi, protozoans and worms are all a part of the big picture of human health.