The basic idea is that the human immune system has co-evolved with a number of immune suppressing parasites. Hygiene has greatly reduced the number of these parasites we're exposed to and without them the human immune system is too reactive. That extra reactivity results in our immune system attacking proteins that are harmless, like pollen or peanuts.
So hygiene is definitely extending human lifespans by preventing us from getting deadly bacterial and viral diseases. But it may indirectly be causing auto-immune diseases. The good news is it's not all that hard to introduce safe parasites back into our bodies: http://en.wikipedia.org/wiki/Helminthic_therapy