When people use the toilet on planes, the design of the toilets uses so much less water than a toilet on the ground, in the airport, and how much a flush of water takes.
So if you assume that people were going to use the bathroom regardless, they just saved the processing of a lot of water by doing it on the plane. Probably ounces versus gallons. (~100 mL vs. 1-2 L)
(parenthetical note, sometimes I wonder if a vacuum toilet would become available for home use, it's so effective!)
Now certainly, flying around to use the bathroom used up a lot more energy, but regardless... Also, you might ask whether people tend to drink more than average because they're offered drinks on a plane.
I used to wonder, considering the hundreds of pounds of water/soda/etc loaded on a plane, as people drink and consume it all, wouldn't it be efficient for the plane to dump that water in flight and save the weight and extend the range. Turns out (of course) that is so negligible compared to the overall weight of the plane...