http://ucdmc.ucdavis.edu/publish/news/newsroom/1789 is the only significant study that I'm aware of. My interpretation is that risks are substantially over stated for true "back country" sources in the Sierras and likely most other places where you would find drainage areas without significant human impact. I still filter water almost all of the time but I worry less when I can't for one reason or another.
I don't really disagree. I expect that, as a practical matter, it's pretty safe to just drink water in a lot of remote places. That said, I also filter or use iodine even if I don't worry about medical facility cross-contamination procedures a lot of the time :-) It's not a lot of trouble and the consequences of getting an infection are unpleasant.