Greed started this, let's be honest.
CBS and Paramount see other people profiting off of the copyrights that they secured ownership of, via numerous kickstarter, etc. campaigns. Even if it's 'not for profit' money is exchanging hands and someone is getting paid, be it for rent, construction materials, in some cases salaries, etc. etc.
I'd argue that Renegades has been much more 'in your face' than Axanar is, thanks to them including Chekov as a character, but since Axanar was the most popular with fans (at least monetarily, based on the amount they've raised via Kickstarter, etc.), they were the obvious target, since Paramount/CBS are now seeking greater control over their copyrights.
Which Paramount/CBS have a right to do, as it is their copyright (assuming no issues with the copyright transfer of ownership history - keep in mind that NBC/Desilu originally aired Star Trek). The question is, is the fallout from all this worth it? Numerous fansites have correctly pointed out that through fan efforts, the Star Trek IP has survived through the support of said fans. Sure, not all fans pay attention to fan films and such, but a number of them do, and a number of said fans have participated in one or more letter writing campaigns to keep Star Trek alive.
Axanar has been very vocal about supporting Star Trek Beyond in recent days, as they feel 'indebted' to JJ Abrams and company for sticking up for them. And we don't know difinitively if a 'side arrangement' is in the works (Alec Peters has implied that negotiations are ongoing) and if it any said negotiations will reach fruition. I'd hope that some of the other fan efforts are able to do the same (secure a license of sorts) going forward, so that their efforts to date may continue.
However, that doesn't mean that the diehard fans should let Paramount/CBS off the hook. I STILL say that if a licensing agreement with the various fan effots could be reached, that would be CBS/Paramount's best play. The released fan guidelines could still apply to those that don't want to involve lawyers and such in order to produce their fan film, but for those that want to tell longer stories, a written agreement between the respective studios would do wonders in appeasing the fans, and Paramount/CBS could even get cut in for a share of the profits if there are any.
Of course, however, it all comes back to greed. It would seem that CBS/Paramount feel that they are the only ones that should profit off of their IP, and aren't interested in 'sharing the wealth' so to speak, hence the current situation. I'd also speculate that they feel that they can tell the stories best (note that I strongly disagree, the 'reboots' suck IMHO), and IMHO don't want to be shown up by better scriptwriting and such from some indy project (hence hopefully not haveing to face the embarresment of supporting weak scripts, which Hollywood in general has a penchant for).
I have absolutely no problem with CBS/Paramount making money off of licensing agreements, I just think that they are being too stingy, and hence denying themselves income off of potential new revenue streams (i.e. allowing fan efforts to be licensed, and allowing them to 'profit' off of their efforts as long as CBS/Paramount get a share). The video game industry ST licenses have been revenue streams of sorts for a while now, and licensed fan films could similarly be a small but steady stream of income. Some dollars are better than no dollars, espeically if it increases your IP's exposure to the masses and increases interest in said IP.
As an aside, there are only five OFFICIAL Star Trek conventions in the States currently listed on TrekNews between now and the end of the year, with maybe a half dozen more 'unofficial' ST conventions. Sure, there will be Star Trek actors at other conventions, but those are more generalized events (DragonCon, San Diego ComiCon, etc.). This makes me think that CBS/Paramount may be exerting more control over 'convention licensing' as well (which we wouldn't hear much about), as I remember there being a LOT more of these events a couple of decades ago (nearly one in every state). Conventions have become more centralized as of late, but it's interesting to note nonetheless...
One possibility that I've considered lately is that CBS/Paramount simply aren't interested in catering to the older fans any longer, as we are all getting older, and our numbers are dwindling as we die off. Through targetted marketing, CBS/Paramount CAN build a new fan base from the Millenials and such, and leave us Gen X/Boomers behind (I'd argue that they've done exactly that). Lets be honest, even if ALL of the old fans boycotted future efforts, CBS/Paramount still has potential customers. The Millennials (ages 19-35) are now the largest generation to date by demographics, and over 30% of the US population is between the ages 12 and 35, this includes post-millennials. And ALWAYS REMEMBER that almost all major studios are beholden first and foremost to their owners and shareholders, not to any one franchise they may own. Around HALF of the moviegoing audience these days is aged 35 or less, and younger people are more likely to buy oodles of fan merchandise to boot.
Yes, I'm mixing demographics a bit here (TV viewers vs Moviegoers), but the point is that CBS/Paramount are looking at that younger audience and may very likely feel that those are the people that they will make the most money off of, hence why us 'old fogies' aren't getting catered to as much these days. This is the reason I can understand why the studios might think that their new 'streaming model' for the new series will work - younger kids are more likely to stream content as opposed to watching it in more traditional formats. I think that they are unnecessarily limiting their potential customer base in the process, as not everyone streams. Sure, the DVD's will show up at some point after the fact, but those don't generate ad revenue very well.
I think that CBS/Paramount have miscalculated here, but they are worth many billions of dollars more than I am, so my opinion doesn't matter. I do think that in the case of the Star Trek license, purposely alienating a part of your current fanbase is a mistake... as in cutting yourself off from more profits by doing so.
In the meantime, I'd absolutely LOVE IT if someone created/made available a new sandbox for the fan film makers to play in, with sufficient similarities for the stories to be told in a similar context, without infringing on the ST copyright in the process. Renegades seems to be going down this route now, but universe building takes time, and there are a lot of interesting IP's out there that could use the support...
Sure, the fan efforts would have to retool their sets, costumes, etc., but they shouldn't allow such a 'simple' obstacle stop them from telling/showing their stories in a new light/using a different framework.