When people were confused by the keyboard, Jobs said that death would take care of that. When it came to files, he saw that as a problem that needed to be solved in the system, but I think it is more confusing on the iPad than macOS.
People have had to use files, moving them to floppy disks, burning them to CDs, copying them to flash drives, and now dealing with them with services like Dropbox. I would think files and folders in a home directory would be something people understand now. I think the modern smartphone and tablets made a lot of people regress, and the youngest simply aren’t learning it. The less it’s used directly, the abstract the idea becomes, and that makes systems harder to use, because at the need of the day it’s still files and folder. Avoiding that has so far created confusing layers of abstraction that haven’t worked so well.
I completely agree, and I think this is probably iOS' single biggest design mistake. In trying to hide away difficulties non-power users face managing a filesystem, they've managed to make things both more confusing for novice users and just plain annoying for power users.
I think the issue is that most computer users do understand at least a little about filesystems. They might lose things or accidentally delete or overwrite things, but I think many many people are reasonably okay with the concept "my things are in files, my files are in a folder".
But the app-centric model iOS uses becomes unnecessarily difficult when you need to do anything with a file that extends beyond viewing it in the software that created it. Emailing or copying a file is an incredibly common thing to need to do, yet some of the most technophobic people I know can manage it just fine on a PC because the process is the same for any and every file. The hardest part for them is usually just remembering where they put it.
That one problem is solved by an app-centric file model, but introduces a much bigger problem in that the mechanism to share or copy a file is different for every app! It might be under an "export" option, or it might be under a little abstract picture of a square with an upwards pointing arrow—because of course, everyone universally understands that square-with-upwards-arrow is how you email this to Steve in accounts...
(Yes the share icon is fairly standard across iOS apps, but it could be and is located all over the place, and I'm not convinced it's intuitive that step one of "emailing a document" is "open Word").
I regularly manage thousands of files in nested folders of website projects as well as Affinity Publisher documents in nested project folders, each with hundreds of linked asset files. And this also includes regular use of local network drives, external drives and sftp accounts for websites.
And many apps are now much more flexible in terms of opening and saving files in locations other than the default. It's not identical to the Mac Finder and there are occasional oddities but in my experience it is very capable. But it's nothing like what it was 10 years ago.
Contrast that to how iOS just generally leaves applications to "own" their own data and present them however makes most sense, with only a few exceptions (the most notable being the Photos app, which sorts and displays photos by things that make sense for photos). The place where you'll find the thing you were working on is actually just in the app where you were working on it, which is, unsurprisingly, far easier to explain. Plenty of people get on perfectly fine without knowing or caring about "files" and are not really worse off for it.
The format topic is also something that I see causing frustration, but it is not complicated to understand, as long as someone is familiar with the concept of incompatibility (screwdrivers, human languages, etc.)
In my opinion at this day and age is more an issue of “never needed to learn / cared to” than that of “it is difficult to learn”.