The advent of modern fandom has perhaps blurred the lines of IP ownership, at least in the minds of fans. I don't mean to suggest that die-hards are under any apprehension that they hold the legal rights to any aspect of the properties they love so dearly; rather, it's a type of spiritual ownership that can create both a heretofore unknown passion in a pop culture artifact and, more harmfully, a sense of entitlement. For some, nothing done in the name of fandom can be wrong, even though the transactional nature of the relationship hasn't changed after all these decades.
Fan-made projects are nothing new, nor are the steps taken by studios and others to take those projects down. The latest instance involves Nintendo and the Legend of Zelda series, which has renewed and reinvigorated its fandom over decades by continuing to put out new and interesting games across four decades. It's undoubtedly had plenty of fan-made games come along, particularly within recent years as technology and access have improved, and one of the latest, The Missing Link, has been shut down by Nintendo on copyright grounds.
As reported by Kotaku Australia, Nintendo filed a complaint against the game's GitHub page, which was subsequently shut down, on the grounds that the project didn't constitute a fair use of the company's work. Missing Link wasn't a wholecloth creation of the team creating it; rather, it was a work stitched together from code pulled from both Majora's Mask and Ocarina of Time, both official entries into the Zelda canon developed and released by Nintendo.
There is perhaps an argument to be made that Nintendo does more harm than good in squelching the enthusiasm of fans, but it would be an easier argument to buy in discussing cosplay or art or any other manifestation of fandom. Nintendo understandably wants to control what is out there as far as Zelda games, and opening things up to fan projects is opening Pandora's box. Granted, it seems unlikely that any new game would diminish the appetite or sales for the actual sanctioned games, but that's not something a corporation as big as Nintendo is going to leave to chance.
Other fan-made games will arise, and perhaps some or even most will get completed in some form and make their way onto the internet, and a different game will begin as Nintendo seeks to shut those down. That seems to be the price that entertainment companies have to pay for the passionate fandom they ultimately rely upon.