One of the advantages to the Steripen is that it kills viruses, and without relying on a filter which can get plugged or run slow. That is one of the reasons I like it, though I don't think the virus factor matters much for typical north american backpacking trips. You don't find hepatitis living in mountain streams in US national parks. It is pretty useful for Third World traveling, though, both in the backcountry and in cities.
One additional advantage of Steripens, too, is the additional nutritional value you get in your water. Filters remove all the little pollywogs and eggs and larvae from the water, which are such a good source of protein. wink