Trying to get my head around setting directories and the like, and I think the best way to learn is to ask a few questions. So if someone has time to help me out-please do!!!

I ask, do a lot of you as designers set up different directories for different aspects of your site. I'm trying to understand why you wouldn't simply upload your files to the/blah/blah/public_html/ or whatever folder and leave it at that. What is the need for all these subdirectories.
( Iam aware of theneed for password protected folders and the like), but why bother with more simple sites.
Could someone give me an explanation/point me to a tutorial explaining all about this.
P.S. Excuse my ignorance on what should be a really simple topic, but hey, you've gotta learn somewhere.