Since I'm the second to vote, I suppose I'll write some comentary...
I hate clutter, especially in home directories. I've seen too many home directories with 100 random files in them... eww.
Not to mention the fact that Perl itself has wonderful directory organizatoin. It could be better, perhaps, but it's pretty dang good none the less.
Windows, in many cases, attempts to hide directory (oops, 'folder') hierarchy from it's users. This way, you never have to know that you've saved hundreds of Word documents related to everything from your thesis to your MP3 collection in the same place ( with a name called ``My collection of MP3's is very large.doc'' ).
At least all your programs ( and their configuration files and dll's, yuck ) are all expected to live under ``Program Files''.
What directory structure? ;-)
You can put anything anywhere without reservation. Put it on your Hard Drive, or heck, put it on your Desktop ( isn't that on your Hard Drive too? oh well.... ). With the exception of a few things ( extensions and, where are those configuration programs anyhow? ) have to be someplace.
On this OS, it's the hardest to enforce heirarchy since you don't 'really' have to have any at all.
I don't want to talk about it :-)