Programmatic vs User Level Separation

While listening to a recent podcast, the speaker was comparing Linux to Windows. He made the statement that Linux has had a problem because its windowing system was not as well separated from the command line interface as MicroSoft Windows. My mouth dropped. When is separation not separation? Programmatically, Linux's windowing systems are much more separated from the command line than MS's Windows is from the command line. However, from a user perspective, the Linux windowing system usually requires much more interaction with the command line than does Windows, especially in the realm of installations.

So, listen up, programmatic separation is NOT THE SAME as user level separation. Sometimes we geeks just don't get it.