"must of knew"... "could of." snicker.
First, do you really think a fan film-maker could ever negotiate a license with a studio? It would never happen. There'd have to be a fundamental shift in the entertainment business. Seriously, the idea that Paramount or CBS would license a fan film the rights to Star Trek some of the dumb shit that Axanar supporters spout. Some even went so far as to contend that doing so "would be smart and forward thinking."
As far as how someone inadvertently makes money from a fan film, it's quite simple, and it's been covered on every other page on this 245 page thread: you crowdfund, fully expecting to use every dime you raise, but raise more than you end up needing, and don't know what to do with the rest. It could be an overage of $5, $5,000 or $500,000. Either way, it's profit.
In fact, a lot of people here contend that this is what happened with Axanar, perhaps even as early as Prelude. Some people have argued that they went in with the best of intentions but raised more than they needed, and rather than refund the overages, they concocted a way to pocket the extra money while saying it was being spent (or spending it on things that weren't truly necessary-- like the formation of a studio for future use, or paying off the rent of property used by their other business).
I'm fairly certain about 2-3 different posters were making this very argument just a page or two ago.