They have to pay the copyright fee for every sub receiving the superstations. Perhaps they have negotiated a better deal with these stations. In addition you may have seen threads that advance the theory that the superstations will go away when analog broadcating ends. I don't buy that but some others do.
DISH subs of course have the option (usually) of ordering the supers as a package or ala carte.
In the end though neither DISH nor DTV is talking publicly about all this. So all we can do is speculate.