Here's a news flash: The stuff that comes out of your body during a bowel movement doesn't smell very good. Bathrooms, especially the communal versions that see a lot of foot traffic over the course of a day, often take on a peculiar smell. You can do your part to cut down on the funk by flushing at least once during the course of your stay on the pot.
Forget the tree-hugger types who bemoan wasting water with a courtesy flush. There's a certain efficiency in the mid-sit flush: It helps prevent waste from clinging to the bowl, an unfortunate situation that would otherwise require more flushes down the road [source: Schulz].
Think of the courtesy flush as a form of paying it forward. If you have the decency to cut down on your own stench, others who use the same bathroom will do it too. That means you won't have to get a whiff of what Jim from Accounting had for lunch when you hit the stall for your afternoon "break."