The same applies if you are talking about soft covers like vinyl, or textured. It should be a solid smooth surface if you are going to use clay. a soft brush and cleaner for vinyl tonneau covers is best.
I would think if the tonneau cover is smooth paint matched to the truck then yes I would treat it just like a hood or trunk lid. However, if its one of the textured, hard plastic or soft vinyl ones I would use a material specific cleaner and protectant.