Everyday we work with multiple application windows. You can perform various tasks in parallel. For example, you can read article on one window and take notes on another window.
The Desktop metaphor has been in existence for decades and is often correlated with the user desk at home or office. Often, a physical desk becomes piled-up with notebooks, pen, paper, files and more. The same picture is common in the desktop environment. Files and folders accumulate on the desktop, too.