Years ago, I used to chat with some of the people that were making "Star Trek: New Voyages" (before it became "Phase 2"). I was told at that time that they were barred from having any advertising, selling any DVDs or other merchandise with any association to Star Trek. I remember seeing some of the cast at Dragon*Con around that same time (Jeff Quinn and John Kelley, if I remember correctly), and they were selling autographed headshots of themselves at the con -- not in costume, mind you -- but of them. I always thought that this was part of the deal with Paramount.
At the time, they did not accept donations in any form other than Home Depot gift cards -- I think that was the workaround to get the sets built without angering Paramount about receiving cash for their venture.
I also know that when I was doing my own Kickstarter campaign for my puppet movie that one of the criteria for your campaign was that you either owned all copyrights or had permission to use said copyrights in your campaign. I would think that this would apply to all of the Crowdfunding sites, so I'm rather confused as to how Phase 2 and Renegades are currently running campaigns. It seems like they'd have to have CBS's OK to be able to have their campaign, but at the same time, it also seems as though that is in direct violation of the no payment for these fan films.
Profit or not, I'd think in the eyes of Paramount/CBS, this is money that fans could be spending on licensed Trek merchandise rather than on fan films.