There's still a difference between having things in a defined place, and randomly hurling your mouse around the screen and clicking wildly to find something. Wouldn't you agree that the Windows 8 Charm bar is less intuitive than menus with visible labels?
You won't see me arguing a command line is equally intuitive as a GUI, either. You have to know what to type into a CLI, which makes it less intuitive than GUIs with things you can see and click on. At least if you're an English-speaker, the GUI is usually labelled in English. "ls"* and "cd" aren't exactly vernacular words.
*Interestingly, neither the man page nor Wikipedia mention what "ls" actually means. My guess would be "list screen"? man ls says "list directory contents."