I think CBS understand that if they come down too hard, they risk making the fans really angry. They realize, perhaps, that these fan productions aren't coming out every week and aren't a real threat to their official stuff.
CBS isn't concerned with the feelings of fans who follow Star Trek fan productions. Hell, once the new series is out and available, I can guarantee you'll have the usual split of existing Star Trek fans who love it, hate it, and then the brand new fans who like it and have it as their intro into the 'world' of Star Trek.
Any decisions CBS makes or caries out with regard to fan films (and I'm not in any way predicting they will or won't do something down the road) will be made as a strictly bottom line business/legal decision; and done because they want to protect the Star Trek IP and Licencing/Merchandising of the Star Trek IP.