I've been coming across discussion of this elsewhere.
The scuttlebutt - and these, I should point out are unsubstantiated, so please take them with a grain of salt or disregard them as outright rumormongering, if you'd prefer - reads thusly:
Axanar Productions did so well with their Kickstarter campaign, that they purchased camera, sound, lighting, and editing equipment, and studio space - capital investments that readily breach the not-for-profit threshold that CBS/Paramount have used in the past to tolerate fan productions.
Beyond that, there have been additional (again, unsubstantiated) rumors of general hubris and unprofessional arrogance from the filmmakers.
Such much so that what is known is that Tony Todd, who features heavily in Prelude to Axanar, detached himself from the project well before CBS/Paramount threw the hammer down.
Again, is any of this true? Maybe the truth lies somewhere in between.
But it's not likely that Paramount has any concerns that the general viewing audience would watch Axanar instead of Beyond. There simply isn't a broad enough fanbase invested in fan films to make any serious dent in the multimillion dollar returns that Paramount can reasonably expect from Beyond.
And moreover, how many Trekkies - anywhere on the spectrum from casual to hardcore - would you imagine seeing Axanar and not Beyond? Even in spite of the general grumbling from the fanbase about the Bad Robot approach to Trek?
For what it's worth - it's not likely the Axanar filmmakers are going to be for want; at the very least, they have a bloody awesome sizzle reel to shop around for their next gigs.