Firstly, let me say that water treatment is a personal choice regardless of the validity of the Rockwell article.
Secondly, accurate information is vital to make a reasonable risk assessment. Unfortunately, most of the key points Rockwell makes are critically flawed. They do not represent mainstream science, good science, or even good critical thinking.
Thirdly, discussion should be encouraged. The article as posted on Whiteblaze allows no comments which is especially bad because it presents misleading medical advice without giving readers a chance to respond.
The Whiteblaze intro to the article says Until someone publishes a study about the Appalachians in particular, there is not much data out there at this time about overall water quality along its length.
There has been a very good study on A.T. hikers: Medical Risks of Wilderness Hiking It says in part In a prospective surveillance study, 334 persons who hiked the Appalachian Trail for at least 7 days (mean [+/- SD] length of hike, 140 +/- 60 days) in 1997 were interviewed. ...Diarrhea is the most common illness limiting long-distance hikers. Hikers should purify water routinely, avoiding using untreated surface water... It found, by following the actual results of treating/not treating of water on the A.T., that those that treated water were significantly healthier as a group. To me it makes no sense to post a poorly researched, inaccurate, non peer-reviewed paper focusing on the Sierra, when there is a well-researched, peer-reviewed scientific paper focusing on the Appalachian Trail.
Rockwell quotes TR Welch who said Neither health department surveillance nor the medical literature supports the widely held perception that giardiasis is a significant risk to backpackers in the United States That is absolutely false. The CDC specifically refutes TR Welch's writing Although the advice to universally filter and disinfect backcountry drinking water to prevent disease has been debated, the health consequences of ignoring that standard water treatment advice have been documented Multiple, peer-reviewed papers have shown a link between giardiasis and not treating backcountry water. Welch and Rockwell are the source of the lion's share of giardia misinformation.
I could continue but will keep it simple for now. I have written more with many links to scientific studies on giardia and water treatment for backpackers.
Why Rockwell's Giardia Paper is Bad Science
Debunking a TR Welch Giardia Paper
Waterborne Giardia for Backpackers: No Myth