Paramount understands the importance of the fan community when it comes to Star Trek. They do keep a pretty good lock on the trademarks, but are very reasonable about licenses for merchandising and whatnot, and allow fans to do pretty much whatever they want as long as they don't charge for it.
I used to work for a hypnosis show, and we did a Trek themed version at conventions. At one point, they found out we were getting paid for it and sent a cease and desist letter. We sent them back a copy of a letter we had received saying "love the show, keep up the good work"- signed by Gene Roddenberry. We never heard from the lawyers again. I'm quite certain that if it weren't for that letter, they would have crushed us, but even a casual endorsement from the creator was enough for them to drop the matter.
Point is, they're actually doing a pretty good job at balancing protecting their IP with letting the fans be fans (and GROW their brand).