If, hypothetically, we dramatically reduced the prevalence of airborne disease, what would the effect on our immune systems be? Some hypothesize that living in too sterile an environment leads to autoimmune diseases, since the immune system is calibrated to a certain baseline level of activity, and will turn on the body if this level is not met by external pathogens.
If it turns out that actual pathogens are necessary, and we can't use the kinds of harmless bacteria that get sold as "probiotics", it would still be better to identify pathogens with optimal risk:benefit ratio and determine the optimal dose. Exposure to wild pathogens varies widely, so very few people will be lucky enough to have the best exposure.
Our hunter gatherer ancestors living in bands suffered from drastically fewer respiratory diseases than we do, you need a large connected population for something like the flu to survive in a human population in the long term. The issue with sterile environments is about the lack of random bacteria, not human adapted pathogens.
That’s likely true, but our hunter gatherer ancestors also saw way more water and foodborne pathogens, not to mention continual parasitic infections to more than make up for the relative lack of immune system stimulation from a lower level of airborne pathogens.