From what I can read in the article, it sounds like it's less a "water" issue than a "surface cleanliness" issue. I mean, the same water is coming out of both. To me, the question this little science project addresses is whether the spigot or the toilet bowl rim has more bacteria on their surfaces. I wouldn't be surprised if the actual water shooting out of the water fountain and into their mouths has very few bacteria in it from the spigot.

Stretch raises a good point about what kind of bacteria is involved. We don't know, from the article. Another unkown that I just mentioned is the number of bacteria in the actual water. We're exposed to bugs that can make us sick every day, but usually in such low numbers that our body's natural defenses (like stomach acid) handily keeps most of them at bay.

Pete mentioned some very interesting results, including the results of some interventions. However, the school may not have these electrically powered, cooling water fountains with holding tanks. Maybe they're just the kinds that are hooked directly into the water system. Ahhh, all those fond memories of gulping down a bellyful of water at recess...