Brandon makes some good points.  I'll add a couple points of my own that
some may take for granted:

o For a user interface to be friendly, it has to in fact be runnable. 
Window system interfaces tend not to work well on text consoles or in
environments where the user is running on a different machine which for
various reason't can't display a remote X session from the server.  Some
sites have draconian policies against X libraries even being installed
on servers

o An increasing number of graphical interfaces these days are being done
with gtk/GNOME, which effectively limits them to running on Linuxes. 

Of course, the existence of a graphical interface doesn't really
preclude the continued existence of the CLI, but one might worry about
the latter being deprecated.