As I understand it, our immune systems are pretty busy even under today's sanitary conditions. We're constantly fighting off bacterial and viral invaders, 24x7. But, I guess we're just not as busy as we could be.
The modern western inland diet contains a lot of wheat and other grains which have more omega-6 than omega-3 polyunsaturated fatty acids. PUFAs are used in the synthesis of immune factors (interleukins, cytokines, ...) and this imbalance in the omega-3:omega-6 ratio causes more aggressive versions of those immune factors to be produced.
Then there’s sugar, processed food, work stress, particle emissions, microbes in indoor air... there are plenty of reasons for our immune system to attack itself.