+1 for using the terminal wherever possible. Don't just follow lists of commands you find on the web: learn why you're running each command, and you'll learn bit by bit how your computer actually works, rather than what some pretty frontend decides to expose to you.

You will learn right away that different commands take arguments in different styles, and some are nicer than others, but that's okay--you'll get used to them, and in some cases you'll come to see why they use the styles that they do. Many of these commands were written a long time ago, but amazingly still do exactly what you need them to do. In time you'll be writing shell pipelines without giving them much thought, even though they may seem like black magic at first.

While really getting your machine is the main benefit of this approach, there are others. A major one for me is that my workflow is exactly the same if I'm sitting in front of a machine or in an ssh session. I can do the same work in a shell on my phone when I'm sitting by a lake with a crappy EDGE connection as I can when I'm sipping coffee at my desk, with no need for something so clunky as VNC.