As far as New Voyages goes, some of the actors actually appeared in the new Star Trek movies. CBS / Paramount have a standing policy that as long as no money is made off of fan productions, they're fine (with appropriate disclaimers that Star Trek is owned by them, etc. etc.). Given that so many fan fiction tropes (Mary Sue, slash, for example) developed from Star Trek fan fiction, and the fervor of the fan base, this is a sensible policy.
NCSoft has demonstrated that they have no such policy, with their shut down of other games' servers. Maybe attitudes have changed, but even if personal attitudes are different, it would probably look bad if they allowed a CoH server, when they have previously shut down Tabula Rasa et al.