It really is a personal preference thing. I don't like the look of bare bottom tanks. Like others, I think it looks unnatural. 1 inch of sand makes the tank look nicer and is easy to keep clean if you have snails. That's another downside to bare bottom tanks -- you can't keep livestock that burrow or live in the sand. Nassarius snails for one, but also many types of fish, sea cucumbers, etc.
Like Brian, I have also seen bare bottom tanks that have the bottom completely covered in corals that are attached and growing on the glass. That looks way cool. But that's not really bare bottom, is it? :) When I think bare bottom, I think just the glass.