When (or if) backcountry water is safe to drink without treatment has been endlessly debated on these forums.
The key requirement for what I suggested was very low risk water isn't "clear" or "fast-flowing" but "at elevation in a [designated] wilderness area," (e.g. not the Appalachian Trail, or on rangeland); and "collected very near the source," (e.g., I know it's coming out of the ground without crossing human or game trails before the point of collection). Does that describe the water that made you ill?
"Clear" *does* mean the water has no algal or bacterial biofilms. "Fast-flowing" (if close to an underground source) *does* mean the water is likely to be as cold as it was coming out of the ground. It's been a long time since I had a food handler's card, but IIRC, cold temps inhibit the growth of pathogenic bacteria.
The risk of waterborne viruses in the American backcountry is virtually zero. And (again, IIRC) the organisms of most concern in backcountry water aren't bacteria, but giardia and cryptosporidium. The CDC says both parasites are spread by fecal matter--water under conditions where I would likely drink it untreated is *visibly* very, very unlikely to be contaminated by human or animal feces.
This isn't about being macho, or laughing in the face of danger, it's about rational risk assessment. It's also about cultivating a philosophical attitude that wild nature, while certainly indifferent to me, is not an actively hostile force I need always protect myself from. For me, an antidote to a "pack your fears" approach to wilderness is worth the (very slight) risk of drinking raw water under particular conditions. Others may make a different choice, of course.
I assume your "1 in a billion chance" remark was meant hyperbolically, since the best filters still won't get the last one out of every billion organisms in a contaminated source. And you'd have to drink "1 in a billion chance" raw water every waking second of your life to have even odds of catching anything.