Thinking about it, it seems more dangerous to place the rocks directly on the glass, no? Even if you use some of those wonderful acrylic rods or whatever like in that post on these forums ... you have to think about weight distribution. When you sit the rocks on the glass, it doesn't distribute all the weight evently. The rocks are actually probably resting on like 3 or 4 points, sharp craggy outcroppings. Think of how many pounds of live rock/base rock you're going to stick in. Do you really want 50 pounds of rock all focusing its weight on just a few points in the center of your aquarium, which is already pressured from water (8.5 pounds per gallon) as well as sand (another 100 pounds maybe).
Seems like a good way to break out the bottom glass. Setting the rock on the sand distributes the weight evenly. If you take care to set them up in a way that will reduce the chance of a tumble in case of a shift, I think this is the way to go.
But then again, I am still setting up my first reef ... no experience.