I'm using the exact same sort of arrangement as Capt. Probably about 50% of the bottom has sand and it's there for looks. Plus I love the interaction certain livestock have with substrate (i.e. my pistol shrimp and goby pair, or my cave gobies). You couldn't have these critters in a barebottom tank.
Bare bottom is easy to clean but you pretty much HAVE to clean it all the time to keep it looking nice. Sand gives you a little wiggle room since it can hide debris - but that's obviously a double edged sword, because you don't want the debris just sitting around rotting.