Real world filing cabinets are not infinitely hierarchical, they are very flat. I don't think I've ever seen someone use a filing cabinet with nested folders. You have one list of alphabetized folders with the files directly in it. In this way I think the current "folders" solution in the home screen more closely matches what people expect.
When you have to drill down through more than a few levels of hierarchy to get to what they want, it becomes confusing to keep track of, especially because folders create groups of arbitrary types so everyone has to build their own hierarchical system for each type of data. So while my nested folders for photos represents year/month/event my nested folders in my music library mean artist/album and my Documents folder is a mess where I try and make up groups of things I will remember again later. "does this piece of writing belong in my Essay folder or in my Journal folder?" Who can say? and if I pick one now, what's to say when I go looking for it later I might not categorize it differently?
Things like iPhoto make those decisions for you, just add your pictures to it and it will make you group them as an event, and that is all you have to do. iPhoto actually lets you look for photos in several different ways then: hierarchically by year/month/event, event in overall order, by who is in the picture, or where it was taken. That is a lot of flexibility that lets me search for a photo in whatever way I'm thinking about it in the moment, rather than having to search for a file based on however I originally decided to organize them on the file system.
A straight hierarchical file system is pretty limiting: it only allows you to find files based on one organizational method. That's why search is becoming so useful and why tagging seemed like such a good idea. It would be great if we could find out what the best way for me to keep track of my writing is without me having to think about how it is structured on disk.
So I guess what I am trying to say is that I agree with you that we need different organizational methods for different pieces of data, and that I think nested "folders" is going to be the right solution very rarely. And I agree with Lukas that there needs to be a lot of work done to help people share files and move files to and from the iPad easily.