Why? Because if I pick up the remote (which is symmetrical along two axes) in the dark, and I fumble for the volume controls without looking at the remote, the way I know I've got it upside down is that it doesn't do anything when I press the buttons. Then I can just flip it around and I'm in business.
I had this problem too, until I got a strip of neoprene tape and applied it to the back side top (top being defined as the end that spouts the IR). Now when I pick up the controller, I can feel the strip and know which end is which. Plus, the tape lets me set the controller on my horizontal dash and it not slide around. Multi-purpose!
(O|||||O)