You're welcome to that reaction. I'd recommend the book "Immune: A Journey into the Mysterious System That Keeps You Alive" by Philipp Dettmer.
It has a whole chapter on the hygiene hypothesis, which parts have been debunked, which parts have weak scientific evidence, and which parts have strong scientific evidence.
I don't think I wrote anything out-of-line with mainstream science. It might be wrong -- scientific knowledge progresses, and we're still learning a lot -- but it's not "paleo diet" junk science.
The key mistake you're making is to assume the immune system benefits from some form of "fitness;" it doesn't. It's not a muscle to be exercised. Diseases harm you and getting sick is not good.
There are exceptions.
The key thing to remember is that the immune system does most of the damage to your body in most diseases; viruses and bacteria rarely kill you, since collateral damage from your immune system fighting them usually kills you first. There's a fine balance of how active the immune system ought to be. Parasites dampen your immune system. We co-evolved with parasites, and without them, your immune system is a little bit overactive (which may contribute to the massive recent rise of autoimmune diseases, allergies, etc.).
We know that modern diseases aren't helpful because at this point, we understand how they work. Modern viruses and bacteria -- which evolved with civilization -- are incredibly specific to humans. They "spoof" signals your body uses, for example to modulate the immune system's response. Historically, we'd have diseases which attacked many types of animals, and didn't do that; those were very different.
To give an analogy to defending a city, there's a difference between a broad attack and a targeted attack. Classic diseases are a bit like invaders at the city walls. Modern diseases are a little bit like spies and saboteurs.