A lot of good comments here. And yes, I did notice that the steripen doesn't actually kill things, right before I drank a bottle of sterilized water with little things swimming around in it. As a vegetarian, I have to say I felt a pang of guilt for swallowing them all live, but my water source was severely limited to nothing else by drought. Yes, a filter would've been better!
It has been interesting to talk to backcountry rangers and trail workers in the Sierra the last few years who never treat their water, even if that isn't officially expressed Agency Policy. So perhaps it is true that the reason our purification methods always seem to work is that our water sources actually have nothing in them to infect us: no objective test there.
Then again, maybe we don't get sick because we have such healthy gut floras and immune systems from backpacking and sleeping, cooking, and sitting in the dirt everyday! Truth is, I kind of believe that argument to have some validity!