Ok, I see what you are up to...
When you click the Computer icon, it opens another instance of Nautilus at a "special locaction". This location tells Nautilus to display special content.
When you just execute the nautilus command from a terminal, it opens nautilus as a normal file manager for the current working directory -- /root, the folder you are in.
(by the way, don't fiddle around with your system as root! use your normal user account instead!)
I don't have Nautilus installed, so I can't test it, but you should be able to give nautilus this "special location" as an argument on the command line.
This special location is called a URI (Universal Recource Indicator), and is used in all kinds of applications.
Have a look here:
These are some URIs nautilus understands. Try some of them out.
Type for example $ nautilus "start-here:///"
in a terminal and see what happens...