I think this gets reported all too often as "fact", that being cleaner
causes more diseases, when in fact, its a hypothesis and it has some glaring holes in it.
I found this very interesting review of the hygiene hypothesis.
This became of interest to me today when I posted about the Aspergillus in pillows and someone immediately refuted it saying it is only because we're "too clean" that we have problems. Bleh!
Here's a snippet from the conclusion:
Developing a rational approach to home hygiene
Regardless of whether the hygiene hypothesis is correct, the popular interpretation that ‘dirt is good for us’  has considerably influenced attitudes, and caused loss of confidence among the public regarding home hygiene. One positive benefit however is a recognition by public health professionals of the need to provide clearer guidance. One of the concepts which we need to clarify is the difference between ‘dirt’ and ‘germs’, and between ‘cleanliness’ and ‘hygiene’. Without knowing the nature of the microbial exposure which may be critical for immune priming, it is difficult to reformulate hygiene policy, in favour of improving immune function without compromising protection against ID. Even if we had the correct information, selective targeting of hygiene interventions, as a means of maintaining beneficial microbial exposure, would only be an option if their mode of transmission were significantly different from that for pathogens. If it were proved that intense infection is an essential factor, the evidence suggests that encouraging such exposures would cause significant morbidity and mortality; if the main effect was, for example, a reduction in hayfever, with little or no impact on asthma, the ‘trade off’ would represent a very poor bargain. If it turns out that more general ‘background’ exposure is needed, e.g. organisms with low invasiveness or virulence, such as the rapid growing saprophytic strains of Mycobacteria, the idea of ‘right’ and ‘wrong’ types of microbial exposure is academic, unless we could engineer the ‘right’ exposure, without introducing dangerous organisms. As untreated water may contain up to 109 mycobacteria per litre, the difficulty is how to preserve the ‘friendly’ species while removing those likely to cause disease. One option that is already being pursued is an attenuated vaccine containing the ‘right’ type of microbes (e.g. saprophytic mycobacteria), and there is evidence of efficacy of a vaccine strategy in animal studies  and in some of human trials [245, 246]. With vaccine strategies, there is no conflict with hygiene.