In the past CBS or Paramount have used back channels to stop fan efforts that they felt went to far (a line only they know when crossed) but according to a statement from Alec Peters, no such effort was made here. He said "I was disappointed to learn about this through an article in an industry trade. For several years, I’ve worked with a number of people at CBS on Star Trek-related projects, and I would have hoped those personal relationships would have warranted a phone call in advance of the filing of a legal complaint."
I suspect the lawsuit is a combination of dislike of the Axanar project, Paramount's Star Trek 3 and 4 films, along with CBS's streaming Star Trek series in 2017 with a mix of new executives at the top that do not like, understand and/or care about current Star Trek fans as their real goal isn't retaining the current ones but getting new ones in the desired demographic of 18-54 years old. No explanation from CBS or Paramount on why this fan film and if this represents a sea change on how the two companies will treat fans from this day going forward. Based on CBS and Paramount's treatment of fans and their Star Trek projects in the past, I really do not think the companies have negative intentions. Despite the unlikely intent to harm the end result will be the same. Few can afford a lawsuit, even one that will likely be settled so this day will mark the end of Star Trek fan films and TV episodes for the foreseeable future. How this lawsuit will propagate to other spheres of Star Trek remain to be seen but the net result is nothing but negative for Star Trek and its fans as a whole.