To me, Williams score is specific to Christopher Reeve's Superman. It worked well in Smallville because that was a television show and it made a point of making nods to the earlier movies. It doesn't work for Cavill's Superman which is a very different take--and including it in future film score projects would similar to Superman Returns. It just wouldn't work. This takes nothing away from the brilliance of Williams' score and does not diminish his status as being one of the greatest composers.
The Trek themes are different, because Trek is about more than a single character or a single ship--it is about the universe in which the shows and movies are set. I enjoy how both Goldsmith's and Courage's themes have been reworked over the years.
I think the Williams theme is the defacto Superman theme just as the Monty Norman/John Barry James Bond theme is to that character.