A bathroom can also be called a restroom. As the name, suggests it's a place where you can rest. Thus it's a logical place to have a save point! Few games have functional bathrooms and fewer games let you save in them.
Some games have toilets as the only save point. For example, in Dead Rising, you can only save by going to the bathroom. The use of the bathroom varies in different games. In No More Heroes 2, your character sits down on the bathroom and does his business. Once he's done doing what he had to do, he gets up, zips up his pants and can continue his adventure. In Dead Rising, you can choose whether to go in a stall or in a urinal.