What really sucks is this is the first time I knew it was ever up for download. I thought they were still just doing it in theaters. Fortunately, the torrent is pretty easy to find.
Anyway, why should a particularly well-made fanfilm be any different than fanart? Legally, they're exactly the same, as you're using copyrighted characters, places, and situations without the express permission of the copyright holder, but Nintendo has never sent cease-and-desist letters to people who draw pictures of Mario. And it's not just that fanart is much more ingrained in the internet and culture as a whole (due to still images traditionally being much easier to host online than videos, and pictures being simpler to draw than a decent-looking film is to make) thereby making it much harder to stop. Nintendo hasn't just been complacent or apathetic about fanart or overlooked it because it would take more effort to stop than it's worth, like they usually are (in praxis) about roms -- they embrace it! In principle, HoT is just a scaled-up version of the colored pencil envelope drawings that used to grace the borders of Player's Pulse.
I understand the need to prevent genericization, and agree that people probably shouldn't be making any money off of properties they don't own (part of me wants to say that BMB along with others deserve what money they can get for their effort, but if you say that, then it's tough to still make it illegal for Warner Bros to go and make their own Zelda movie without ever consulting Nintendo and make millions off of it (let alone steal the stories you write yourself and turn them into movies without you getting any money) without drawing some very poorly-defined and rather ethically questionable lines), but still. George Lucas, for all his flaws, has shown that it's perfectly possible to make buttloads of money while still letting your fanbase do whatever semi-illegal stuff they want so long as they don't use your stuff for profit or porn. Why can't our fandom be like that?
There are several possible interpretations as to why this got shut down while fanart is fine. One is that they're afraid that HoT, unlike most fanart, is professional-looking enough that people might not instantly know it's a tribute and not official, which could be taken as a big compliment to the BMB guys. Another is that there actually is a nonzero chance of Nintendo someday making their own Zelda movie, and so they had more legitimate reasons to care about this than pictures (even really good pictures). And yet another is that there's no chance at all of making a movie -- perhaps Nintendo regularly looks through fanart to find new 2D artists to hire, and therefore they allow it to continue as a free recruiting tool, but since they're never going to make a movie, they have no need of filmmakers, and can freely crush them.