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There have been several studies of water quality in the Sierras, and the findings are that in general, treatment isn't needed:
http://www.yosemite.org/naturenotes/Giardia.htm
http://www.wemjournal.org/wmsonline/?request=get-document&issn=1080-6032&volume=015&issue=04&page=0238
http://www.yosemite.org/naturenotes/DerletWater.htm
The correlation between human/backcountry use and contamination seems to be fairly weak, while that between stock animal/grazing use and contamination is stronger.
Despite these studies, one reason to treat the water is that you could be unlucky enough to obtain your water a few hundred yards downstream of a dead animal that's contaminating the water. Another would be if you know you'll be obtaining water downstream of an area with active grazing or heavy stock use.
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