In a series of extrinsic tests, the court pitted the Axanar project against the tenets of fair use law, and ultimately found it to be "substantially similar to the Star Trek Copyrighted Works." Specifically, the ruling cites the accurate portrayal Klingon and Vulcan physiology compared to official works, the clothing and culture of fictional species, locations from the original series such as specific planets and starships, and more. Klausner spells it out pretty clearly, stating that the Axanar crew "expressly set out to create an authentic and independent Star Trek film that [stayed] true to Star Trek canon down to excruciating details."
For Klausner, the case is pretty cut and dry. The work is clearly not a parody, clearly uses the Star Trek brand and, according to the judge, does not qualify as nonprofit because -- although it was going to be distributed for free -- was intended to drive non-monetary benefits for the creators such as future job opportunities.
This places the ruling of copyright infringement clearly in favor of Paramount and CBS -- but the issue isn't closed. Despite settling the question of fair use, the question of intent still hangs in the air: Did Axanar's Alec Peters show a 'reckless disregard' or 'willfull blindness' to copyright, or did he genuinely act in good faith? That decision will move on to a jury trial. Here's hoping Peters' peers don't come down on him too hard for loving Star Trek too much.