You cover the boat to keep the snow and ice out of the cockpit and scuppers. If the scuppers clog, rain or snow melt might run over the sill into the boat. A side benefit is some protection from acid rain,uvand just plain dirt. One bit of advice is not to use those blue plastic tarps since they will not hold up. Your choice is to have canvas tarp made or to take a generic tarp and fit it to your boat using those simple grommet makers found in the catalogues.
In either case here on the Chesapeake it is a real good idea to cover