In ScienceDaily recently: "Humans may be susceptible to allergies, asthma, and autoimmune diseases because of increased hygiene, according to Kathleen Barnes of Johns Hopkins University. Without being exposed to intestinal worms and parasites, as our ancestors were, our immune systems are hypersensitive.".
I don't think "hypersensitive" is being used in any technical scientific sense here. Let's make a few relevant observation:
1. It is natural to think of parasites as having a wholly negative effect on the host. But look at it from the parasites point of view. The host is home. Do they want to destroy it? No. In fact if there is something that the parasite can do for the host without too much cost then they might do it. This won't mean much if the parasite is rare. But suppose it is common, as intestinal worms have historically been. Now if the parasite does some beneficial job, then the host has no selective pressure to maintain an independent capability to do that.
The good-bug/bad-bug dichotomy is often wrong. Heliobacter Pylori is a typical case. It was found to cause ulcers. Yet it is nearly universal in humans. So there is some deeper disease process happening when it causes ulcers. And getting rid of it might also cause other problems.
2. In support of the "hypersensitive" theory: It is true that human worms have learned to somewhat suppress the human immune system. So removing them may well make it hyperactive, and thus more likely to attack common environmental stuff, and self. I'll be surprised if this simplistic fact turns out to be the whole story or even the main story.