Ownership

[morpheus]

> Another big reason is that it keeps misbehaving applications from screwing
> things up too. Maybe there's a security bug in one of the multiple libraries
> linked into your GUI file manager, and when you click on some untested
> downloaded file as root, surprise, it's got a exploit. This is much less
> likely to happen with cp, mv, or rm.
> 

True, using cp, mv and rm from the command line is the safest way to go
if you need root to access the files.
Some people are intimidated by the command line, others just find it
tedious when copying lots of files from different locations.  However,
using the -i (interactive) and -v (verbose) options usually prevents you
from accidentally copying in the wrong direction or overwriting
important stuff.