Actually this is something I've always wondered about as well, and many a debate has stemmed from this topic. The way jamil explained it, and other experienced members in one of my clubs also agree is as follows:
Bacteria and wild yeast lives in our water and pipes. While these microbes are harmless to those of us consuming the drinking water, they will do detrimental damage to the beer. For those doing partial boils it is recommended that the brewer boil his top off water for 15 minutes to ensure it sterilized.
With that being said there are many brewers who top off with tap water with no adverse effects. Of course just because we can't taste an infection right off the bat does not mean it does not exist. Some infections can result in low attenuation, poor fluctuation, flat or silky mouthfeel, and of course terrible aging qualities. It may take 2-6 months for the bug to really become evident in a beer, especially to an untrained pallet. If I keg a beer and let it cellar for 6 months to a year and come back to find a very well aged, mature beer that tastes clean, I'm quite pleased and I know my sanitation procedures are up to par. If however, in a year I find that beer developed sour notes, wet horse blanket, barnyard, wine viscosity then I know I've got a problem unless of course I added Brett to the conditioning vessel; then I'm right on target.
I'd rather not take the chance. 15 minutes always seemed like a reasonable sacrifice to ensure a clean beer would be enjoyed.
I think in fact Palmer and jamil talked about this very topic in depth on "brew strong." check the archives, and you can probably find it pretty easily.
