Here is a simple way to help keep rain out of nesting boxes.  If a nestbox is properly built (with an overhanging roof), in most cases, rain is kept from entering the box.  However, wind-blown rain is a different matter.  While it is impossible to always keep this type of rain out of boxes, you can reduce the chance of this happening by simply erecting a box so that the opening to the nestbox faces away from the prevailing wind.