I'll do my best.

What we first need to consider is what a "toccata" is. A toccata is a fast paced piece of music meant to challenge the performer and impress the audience. It was something written less for it's musical substance, but more to show off the performer. Baroque composers (and especially the Classics after him) loved writing in specific forms like toccatas, so when someone went to go to listen to a toccata, they knew exactly what to expect. If you listen past the opening seconds, it follows this form and is very fast paced and not quite as ominous as the beginning.

So why might have Schumann found it humorous? The "grandiose" opening is much different from the parts after it. Listening to the piece as a whole, that bombastic opening does play as a little humorous in retrospect. Bach also writes the beginning in parallel octaves (playing the same note high and low), which makes the beginning sound even more grand. This was a serious no-no in Baroque counterpoint at the time, so Schumann might have seen as Bach playing against the rules. This as well as other "odd" things in the piece caused some Bach historians to at least pose the question that Bach may not have even written the piece.

It's important to remember that Bach had only been in the minds of Romantic composers for a short time. Bach's music was not widely known outside of Germany and had only been beginning to gain prominence at the turn of the century, in part thanks to Schumann's contemporary Felix Mendelssohn famous performance of Bach's St. Matthew Passion in 1829. This helped cause research and rediscovery of much of Bach's pieces. When Schumann wrote the review in 1840 of Mendelssohn performing the piece, it was likely the first time the composer heard it. Dr. William Little of the University of Virginia in the link above claims this review where he claims the piece is full of "characterisitc Bachian humor" is marred with errors and ambiguous in nature. Schumann actually claims in the letter the piece was Bach's Toccata in A minor instead.

A better question might be to ask; why is it so ingrained in our minds as a dark piece? In the early 1900s, movie theaters often employed pianists to play the piano while screening silent films. It was up to the pianist to decide what music to play, so the pianist was either given a sheet music of cues to play with the film, or they had to do it them self. The opening of the Toccata (and not the rest of the Toccata or Fugue) was a common cue in tense, dark, or scary moments in silent films. It was eventually incorporated into 1931's Dr. Jekyll and Mr. Hyde and 1934's The Black Cat, as well as several other films. when "talkies" first started being released. By that point, the opening of the piece was ingrained in popular culture as dark and gloomy.

Schumann was specifically reporting on an organ recital given by Felix Mendelssohn. Here's the page the Wikipedia article is citing. Schumann's actual words (still in translation, of course) were

...which was followed by a Toccata in A Minor [sic] with a Prelude typical of Bach's sense of humor.

We know it's actually a D minor toccata because the program survives. We don't know for certain that it's the famous one, BWV 565, as there is another. But the other one - BWV 538 - would be a much less likely candidate as it's in a very formal style.)

https://books.google.com/books?id=0u5xOkBJpMEC&lpg=PP1&pg=PA56#v=onepage&q&f=false

This CBC article has something to say about how the standard modern connotations of this piece came about. It's largely thanks to Hollywood: the piece was used with grimness, forboding, and horror in mind in the movies Dr Jekyll and Mr Hyde (1931), The Black Cat (1934; a.k.a. House of Doom), The Phantom of the Opera (1962), and many more. It was the Phantom that really cemented its reputation: if you look back at its use in the Disney movie Fantasia (1940), there it's not treated as a thing of horror but as something completely abstract and majestic.

Having said that, the rendition given in Fantasia is very much early 20th century in tone. The fashion for performing Bach in those days, especially among Germans, was to take Bach's music very slow and solemnly. And the arranger and conductor for the Fantasia performance, Leopold Stokowski, took that tendency to an extreme. If you look at the actual score of the piece, it's obviously intended to be very very quick and light: not inexorable, but sparkling. Here's a rendition of the opening bars that I just slapped together in Sibelius without any extra interpretive marks, modifications to tempo, or anything like that: in Bach's day it would certainly have been played more interestingly than this, but it may still give you an idea of how it's written as something rapid and bubbling.

One last caveat: it is very much the standard opinion among modern musicologists that the piece is definitely not by Bach. It is completely alien to the style of his organ music in almost every respect. There have been some attempts to reattribute it to Bach by arguing that it was originally written for a different instrument, usually a five-stringed solo violin or cello - I'd think more of a lute or viol - which is possible: Bach did for example take a fugue he had written for solo violin and rearrange it for lute and organ, and all three versions survive (violin: BWV 1001; lute: BWV 1000; organ: BWV 539). But it's still very questionable. There are many features in the famous toccata & fugue that do suggest it was originally intended for another instrument, but it's no more characteristic of Bach's other solo violin/cello/lute music than it is of his organ music. Finally, yet another possibility is that Bach took a violin/cello/lute piece by someone else and arranged it for organ... but it's still speculation, and there aren't any close parallels for him arranging other people's violin works.