One of the most interesting ideas to have emerged from the study of epidemiology is the 'hygiene hypothesis', essentially an explanation for why there are much higher rates of autoimmune and allergenic diseases in the west compared to developing countries. The concept is pretty simple, because rates of infectious diseases and family sizes in western nations have decreased this has led to a 'bored' immune system. Because the immune system is still developing and hasn't been stimulated like it normally would have expected to (as it evolved in a certain context), it starts to react more vigourously to things in the environment. Two good examples are antigens from innocuous foods like peanuts or aerial antigens like pollens released from plants (causing asthma).
It shouldn't come as a surprise then that numerous 'alties' and naturalists have decided to jump on this hypothesis to promote their agendas. For example, some anti-vaccination groups don't take vaccinations on the basis that the hygiene hypothesis supposedly 'supports' their idea that children should be exposed to potentially lethal pathogens. Of course, this ignores the fact that a vaccine works by stimulating immunity by the same kind of mechanisms as the original organism so isn't really that founded. Other alties have used the supposed support of the hygiene hypothesis to push things like probiotic treatments, natural health remedies and generally disparage conventional medicine.
This of course relies on somewhat of a distortion of what evidence the hygiene hypothesis actually has in support of it. The first thing to note is that the rise in allergies and other immune disorders has generally fit certain trends.
1) Allergies tend to fit a certain trend, where it's actually those in lower socio-economic brackets that tend to have the highest incidences compared to those who are better off [*].
2) It's not 'bacteria' and 'dirt' generally that people require but certain kinds of pathogens. For example, programs to remove intestinal worms like helminths and certain bacterial pathogens like Streptococcus pyogenes seem to be associated with increases of atopy (allergenic diseases).
3) Germ free animals that have been left without any exposure to microorganisms often demonstrate much higher levels of atopy than those unexposed. We will note however, that any establishment of a microflora, which is basically inevitable no matter how 'clean' you are tends to abrogate the increased incidence of atopy. In other words, every day microbes you are almost guaranteed to run into are likely to be protective so there is none of this 'needing to get plague' buisness [*].
So bear in mind that this increase in atopy is being explained not by a lack of 'germs' but rather by specific kinds of predictions. The lack of certain pathogens and the increase in pollution particularly in low socio-economic areas. When you see those alties blaming allergies on vaccines, no 'good' bacteria or other things, it would be best to cast a skeptical eye over the claims to see if they really understand the actual theory first.
*) J.F. Bach, The effect of infections on susceptibility to autoimmune and allergic diseases, N. Engl. J. Med. 347 (2002), pp. 911–920.