Think back to ancient times, before the days of the PC and when 'word processor' was the punchline of jokes. This was the time when 'document' meant something important or legal, like the Magna Carta, and normal people wrote 'papers', unlike modern times wherein even a shopping list prepared in Word is a document.

But I'm getting ahead of myself.

A draft of something written is a variant, copy or revision. Written works could go through a series of drafts before being completed. Generally, the first of these drafts was called the rough draft, not for its texture but for its relative lack of sophistication and completeness. Working from the rough draft, the writer would revise and edit and ultimately produce the finished work. As such rough drafts were often covered in editor's markings, scribbles and red ink.

Now, however, in the days of Word, WordPerfect, ClarisWorks, StarOffice and their ilk, many people prepare their documents start-to-finish in the word processing program. Such a process precludes a formal rough draft. Others, though a small minority, still write a rough draft on paper and then work from that into the program.

and now for posterity, the old e1 writeup:
In the olden days before word-processors, when writing a document, one was forced to often make multiple copies, editing and re-typing or writing after revisions. Now, in the days of Word and WordPerfect (or Notepad, or vi, or emacs, whatever), this step is often overlooked in favor of on-the-fly editing.