As I understand it, Star Trek's movie franchises still belongs to Paramount Pictures, but the TV franchise belongs to CBS. Both will have to come to some arrangement in the future in relation to the production of future films.
There are two different Paramount Television companies - 'Paramount Television', the company which makes programmes, including Threshold and Enterprise, for UPN and other networks, and UPN, the television station which Viacom had a stake in until the CBS merger. Both of those are owned by CBS.
I don't know where this leaves the website - Paramount Digital Entertainemtn was supposed to be lost in the split. Trek book publishing remains with CBS who own Simon & Schuster.
All very confusing... It does make me wonder, though, that should Star Trek ever return to TV, would it be more likely to air on the higher-profile CBS network (where it could get higher audiences than UPN allowed it?)