As I mentioned in a previous post http://onwordsblog.blogspot.com/2009/10/medieval-manners.html
many of our customs such as shaking hands began because of cultural things in the past.
One thing I didn't mention is keeping toilet lids down. That obviously originated because of the need to reduce odors in chamber pots and outhouses.
Now that California is having a severe drought and people are trying to reduce water usage by flushing less often we're rediscovering the practicality of that custom.
But ever since indoor plumbing was invented it has always been considered polite for men to lower toilet seats after relieving themselves and that is not just to be polite.
When I was a little girl I got up in the middle of the night to go to the bathroom and my brother hadn't put the seat down. I sat down in the dark and fell into the toilet. Landing in cold water in the middle of the night is not a pleasant experience. I couldn't help screaming and woke my mother, who made sure my brother remembered always to lower the seat from then on.
Lots of things we consider a matter of manners really do have practical purposes.