The problem with the hygiene hypothesis is that clinical trials to test it haven't really shown any results so far. Coronado Biosciences tried using pig whipworm eggs to treat Crohn's disease and other inflammatory conditions and the result was it showed no impact whatsoever.
Now that's not to say the theory is completely debunked, but so for our theory hasn't really held up with testing.
It kind of reminds me of antioxidants as well. Yes, there is a lot of evidence that oxidative stress plays a role in disease, but attempts at levering antioxidants hasn't shown any impact.