If you put a ground cloth under your tent that's larger than the tent footprint, then all of the rain that runs off your tent fly is going to be funneled underneath your tent. Not good, unless you like sleeping on a water bed, and testing the quality of your tent floor.

To avoid this, just set up your ground cloth so the edge of the tent, or tent fly extends beyond the ground cloth. Tuck the ground cloth in underneath the floor of your tent an inch or so if you need to.