Considering that Thompson is very ideologically similar to Bush, completely supports Bush's policies and has closely aligned himself with and defended Bush, do you really think he can distance himself from Bush in the general? And if he can't, then do you really believe a candidate seen as closely tied to Bush can win?
Bush will be hung around the neck of who ever gets the nod from the GOP. Rudy = Bush with some social liberal views, Mitt = Bush+Mormon+flip flopper, Thompson = Bush+lobbyist+Hollywood+very little experience. Any of them will face an up hill battle against the legacy Bush leaves them (except, of course, with the limited number of folks that still love Bush - I think 25% of them post on this board).
Rudy = Bush will be a tough sell, I think. People have already seen quite a bit of his capabilities through his 9/11 leadership, and will certainly know by November 2008 that he's not a reactionary social conservative.