Why Pipe Organs Sound Scary

They don't, except for when they do

Edit:
So I want to clarify what I said about Bach not writing the Toccata and Fugue in d minor.
There's been a lot of discussion on the subject, and from everything I've gathered the answer is that this piece is one of the more anomalous in Bach's repertoire which, along with the lack of an original score written in Bach's hand, makes his authorship of the piece seem somewhat less that certain by a handful of Bach scholars.
However, until there is more substantive evidence, the convention is to attribute this piece to Bach.
So "Bach didn't write the toccata and fugue in d minor" may have been a little too strong here, maybe even misleading, and I just wanted to take a minute to completely clarify that point.
The quote from Jean-Claude Zehnder is "The matter still remains open, despite the scholarly discourse that began in 1981. Until proof of the contrary, BWV 565 should be considered as a work by Johann Sebastian Bach."

oops.

Sources:

A fantastic source on trying to decipher how much Bach actually appeared in the silent film cannon, as well as some scoring conventions of the time:
Status, Standards, and Stereotypes: J.S. Bach's Presence in the Silent Era
James M. Doering

A brilliant article about the 1931 Dr Jekyll and Mr. Hide, I doubt I would've ever noticed that the organ in the opening was transposed down a minor third and this article shed a lot of light on one of the first ever horror soundtracks:
The Strange Case of Rouben Mamoulian's Sound of Stew: The Uncanny Soundtrack in Dr. Jekyll and Mr. Hyde (1931)

Basically everything you could ever want to know about the narrative themes and significance of organs in films.
I cannot stress enough how valuable this source was and if you're at all interested in what a musical instrument could represent then you owe it to yourself to give this a read:
Carnival of Souls and the Organs of Horror

There are also a LOT of articles that outline the history of the Toccata and Fugue in d minor and its presence in film history, there's just too much to organize and they overlap a lot so I'm just going to link them all en masse here:

[Tehinstrumentalist]

I'm quite satisfied that the reason organs are scary is because of organists. Our tendency to avoid sunlight and look like vampires probably doesn't help the reputation.

[Sananjalka]

Ok, so organs are ancient, unreasonably large, maddeningly complex Eldritch horror instruments and organists are their creepy plotting followers. Got it.

[lordsebasWL]

Organist here, there's a french organist, Louis Vierne, that died in the middle of his recital in Notre-Dame. He had a heart attack and fell on the low E pedal note, dying as this single low note echoed throughout the church. If you need any more proof that organists are hardcore, this is it.

[jdpragmatic]

The organ is often called the King of musical instruments. Essentially, it’s designed to sound like every other instrument. So it’s not that they sound scary, it’s that they sound impressive. They make scary music sound scarier, grand music sound grander, or sad music sound sadder.

Oh And you mentioned “you have to be an octopus to play the organ.” 21:38

[AceSimGaming]

So when the villain is playing the organ he's basically flexing.

[kon]

"Organ players are weird"
Me, thinking about my music teacher, who can play literally anything perfect from sight and who we once saw looking at haunted houses for sale: "yeah, that checks out"

[rajasitorus]

Organist: I play an orchestra
People: Did you mean, you play in an orchestra?
Organist: Nope. I play an orchestra

[AngelicEra]

What I've learned: it's not that pipe organs sound scary, it's that pipe organists ARE scary.

[mac]

As an organist, I found it very entertaining when he lost his mind trying to explain how an organ works. Let me say it gets even more complicated when you try to understand the mechanics to it.

[CossackGene]

Organist pulling out stops: "I'm not even using 50% of my power yet . . ."

[sparkyfox]

“Oh, I play the piano, what do you play?”

“The church”

[unbeatenlake]

“Organists are weird, they play with their feet!”

Davy Jones: *Plays with beard*

[eatornator-oxdx]

Imagine an alien archaeologist trying to deduce human anatomy from the controls of this organ. "Well, as near as we can figure it, they must have had 12 arms (two of them quite long), six legs, and at least three brains."

[portiabartel]

Sideways really said "Organs are scary because Organists are scary"

[peanutgallery]

my s/o has an organ built into his house. it's a perfectly normal house, not a mansion or anything, and then boom... pipe organ. i have struggled to think of a bigger flex.

[oskeewootwoot]

As a brass musician who has spent most of my life playing in brass bands, there's NOTHING in the world like a brass band and organ playing together. Brass bands are already capable of playing incredibly loud, and then you add in the organ...it's immense. I absolutely love it.

[jaggedstar]

"An organ is just a piano with rabies" As a musician I've never heard a more accurate representation of this beautiful instrument

[rob.carrillo]

Video title: "Why Pipe Organs Sound Scary"
Video contents: ORGAN PEOPLE ARE PRIVILEGED WEIRDOS THAT LIKE FEET

[iansaxby]

My dad played the organ in our church. Nobody ever noticed that he was playing "Halfway Down The Stairs' from The Muppet Show before services.

[philclip]

Something else that adds to the mystique surrounding organists is the fact that on many occasions, they are out of our line of sight during their performances. The visual component of performing for an audience is present the vast majority of instruments, but not for the organ. Sound is supreme.