Considering the clampdown on all forms of media in the online world, from file sharing, music, movies, photos, video hosting through Vimeo, Youtube, DailyMotion etc... it was only a matter of time before the powers that be turned their attention to fan films.
It's a bit of an arse they decided to act at this moment (why hasn't this come up before), and at the moment I'm sure all we can do is speculate as to the why... two possibilities (my two cents) could be that either something has happened on this particular production that has just tipped the scaled ever so slightly in a less favourable light than they were willing to turn a blind eye to, or simply it could be a change in administration at CBS, in other words someone new in the higher ups has decided to act, where a predecessor may have elected to let things slide.
Having tackled a fan production development for a different entity of pop culture and later a pilot development, 'and' not getting the green light despite opening a dialogue to establish costs for acquiring rights... when they say no, you just have to step off. Were we annoyed; yes, we tried to go through proper channels and still stalled, but the saving grace was the development didn't go to waste and an original idea is being brought to fruition instead based on a backup concept in case such an event happened.
You have to feel for those that have committed a lot of hard work and effort into this, it did look like an exciting production but it's hard to see how they can continue; creating alternative text, characterisation, macguffins etc, is one way to avoid infringing the copyright and trademarks but then what would it be, it wouldn't be star trek, merely a space war saga, a lot of work to strip out and redevelop, and more importantly defeating the object of the productions outline.
Without trying to sound negative though this almost certainly doesn't bode well for other fan productions, and again for those there would be a lot of time, money, and commitment that would go down the drain. Other question of course is where will it stop... what about Star Wars fan productions, DC, Marvel, James Bond , Doctor Who, will the right holders look at this and start rubbing their chins... it raises serious questions :-/
Matt