The Finder->File->"Make Alias" command is really GUI-only - the actual file is more or less worthless in Terminal.
However, you can make a "real" alias by opening Terminal, typing in
(be sure there is a trailing space), then dragging the folder into Terminal, which will enter the path, so you'll have something like
Code:
ln -s /Users/me/Desktop/Stuff
There will be a trailing space. Finish it with the new location, remembering the path, so it'd end up being a command like:
Code:
ln -s /Users/me/Desktop/Stuff /Users/me/Documents/StuffAlias
Press return.
That'll do the trick; the second name is the alias - it'll be usable via Terminal as well.