While not exactly camp-related in background, when I was an athletic trainer, no, we didn't quarantine them or segregate our athletes with athlete's foot in showers. What we did was ensure that they were using an appropriate med for athlete's foot (usually an OTC cream or powder), taught them about keeping their feet dry (even between toes) and using a foot powder that inhibited athlete's foot. It probably wouldn't hurt to do a daily cleaning in the showers though.
Since athlete's foot likes to grow in places that are warm, damp, and dark, teach your campers to dry between their toes after they shower or otherwise get their feet wet. That eliminates one part of the equation.