A raised design is just much more convenient for smaller coops and has lots of benefits that have already been mentioned. We made ours raised for two primary reasons. 1) It gives us that much more run space which is nice since in our small yard space is at a premium and provides a ready-made shelter from sun and inclement weather (works too...the other day when it was drizzling nasty freezing rain my girls refused to go back into the coop once I let them out, but they did stay under the coop pretty much all day). 2) It makes clean out easier on us because we don't have to bend over to shovel the droppings or shavings out of the coop. We just put a plastic tote under the door and use a hoe to scrape it all out when we do a full change. It also makes checking and changing the food and water in the coop easier. And opening the pop door, since it just happens to be about waist high.
Of course, a raised design also offers a little bit of added predator protection. Raising the coop gives them a place to hide from aerial predators and if the coop is raised high enough it prevents ground predators from using it as cover. If you live in an area that is prone to flooding or standing water, a raised coop keeps the birds warm and dry when the pen is flooded.