Lets imagine different conventions. As soon as you start typing it puts a file in $HOME/Documents (or a configurable alternative). If the application is amenable to guessing a title (like the first entry in Heading 1), then it uses that, otherwise it goes with the usual "untitled". The menu ops are File -> Open, File -> Save, File -> Save a copy, File -> Set name and File -> Move. The last file opens if you stop and restart. Every single operation gets lazy-queued for flush to disk on an activity log (more than just auto-save: preserve every undo-able op). Save means "commit my changes to the canonical copy and clear the activity log".
All of those still use the hierarchical file system. They just use it in a way that makes modern sense.
Users should never really have to worry about saving. Google Docs does a good job of keeping documents saved without any need for user intervention.
Or, lets suppose you just log the undo in a hidden file alongside the original. Imagine you've edited a lot of files. All that eternal undo would pile up, and you'd end up with gigabytes wasted on useless undo logs. Plus plenty of stranded logs from moved files.
No, the ability to save, to not save yet, and to abandon the undo - those are useful features.
This happened to me in 2003 when I switched from Linux to Mac. I still get a little worked up over that, even though nowadays I just let iTunes manage everything and throw away the original files after I rip something.
Also, try plugging your USB hard disk into a different USB port in a different order from your iPod. Now it comes up with a different drive letter and iTunes can't find any of your music.
It might not be the best way to organize most files, but people do understand hierarchical systems. There are too many examples of hierarchies in everyday life.
The filesystem isn't relevant to what either of you want to do - namely, start taking notes, and, not lose them if you forget to save them.
Sure, save them wherever you like however you like - but I bet you start with "I need to make a note of this phonenumber" and not "I need to create ~/data/contacts/business/suppliers/joans.computers" so I can put this phonenumber in it".
Whereas if I'm opening a document just to play around with ideas I won't be doing that, and most documents start that way. I think this is why Word has so far won the field in mainstream document production. Word is a superb tool for prototyping and terrible in almost every aspect of structuring data for its long-term use.
I only save things that think that I'll want to find some time in the future.
As a result, I don't think "I need to make a note of this phone number". Instead, I ask something like "How do I make a note of this phone number so I can find it again?" and then I think "I should put it {some place}".
Yes, hierarchical file systems are merely one of the many ways to implement "{some place}", but that doesn't make "{some place}" unimportant, irrelevant, or unnecessary.
But I do understand hierarchical filesystems, so why would I want to do things the same way as people that don't? I don't use notepad.exe just because vim is too confusing for most people, either.
I installed iTunes once and it took me a couple of confused minutes to figure out that I couldn't play a file in it. First you have to teach the app about all of the music that I might someday want to play, then you can finally choose one of those and play it. But I know where my music files are on the disk and I just want to play them. To use Gruber's analogy, I wanted to type 'print "Hello World"' and it wanted me to start defining includes.
In the same way, I store my information in text files on the disk. They're arranged in a way that makes sense to me. They're searchable, portable, and small. And it works great for me.