Talked with my wife, who herself has started more than her share of 501C's for charitable fund raising and has supervised more than a few nonprofits, and not-for-profits over the years; plus I also spoke with the lawyer she used for filing the correct paperwork with state officials and the IRS, and both came to the same conclusion, Axanar's main problem lies in Ares Studios.
Sure the coffe sales are questionable, as are the "gifts" for donations, but rules for nonprofit/not-for-profit ventures are pretty loose in this regard. For example, as I mentioned earlier, if Hansa coffee was essentially donating the coffee and only charging their cost for the coffee, then giving the rest to Axanar as a donation, then techinically no one has made a "profit" and I suspect Axanar's lawyer would argue that in court. This would also apply toward the "perks" they give for donations. So the question then becomes, did Alec peters use the Star Trek license to make a profit... they will of course argue they did not.
Even paying one's self a salary (which looks really bad), as well payments to the professionals involved would be allowable under nonprofit guidelines. Most people would be shocked when they donate money to a charitable cause how little of each dollar goes toward that cause, and are instead absorbed into "administrative costs." Again, I'm sure that's something Axcanar's lawyer is going to argue.
However, where Axanar has ZERO leg to stand on in Ares Studio. Based on past statements by the crew it is clear the INTENT is to use the studio to generate revenue to create profit-making movies down the road. Between their "Sci-Fi Film Academy" and their option on David Gerrold novels it's pretty clear they plan to make money down the road. Also just buying the property, bulding on it, and rennovating it creates an issue because wouldn't that cause the value of the property to go up? Theorhetically a higher property value is profit... the only way around that issue that I can see if if Alec Peters, out of the goodness of his heart, donates the property to a charitable organization after he's done with it.
What I suspect Peters and comapny will try to do though is argue that Ares will continue to be not for profit and will only pour money they make back into future productions, and use further crowd funding to make their films. Basically Peters thinks he's found a giant loophole in the system and plans to use it to create a career for himself.
When CBS/Paramount first started allowing fan films under the simple guideline that it was permissable "as long as no one made a profit," I doubt, even in their wildest dreams, that they believed any production would be so bold and arrogant with the Star Trek license. Even "big dogs" like NV/PII and STC have run pretty tight ships and have been clear where donations go. Even the "perks" offered have all been related directly to the production (i.e., production photos, posters, scripts, etc.), and not vague, quasi-official looking merchandise that dances a super fine line between legitimate "perk" and licensed merchandise.
CBS/Paramount really was left with no choice but to file a suit.