Unless this is for some educational tool which you are planning to create, in my opinion the best way to learn is just to use it.
To do this you need to know enough filesystem manipulation basics to get started, like:
cd change directory like on Windows
mkdir make a directory like Windows' md (I think? been a while since I've used Windows)
rm Delete a file. Arguments -r for recursive, useful for deleting directories, and -f for force.
ls list the contents of the directory, add the argument '-la' to me a bit more useful
df list the 'disk free', ie. how must disk space you have. Add '-h' for human readable numbers on Linux
Your biggest hurdle is likely to be which editor to use. There are essentially two 'manly' editors, 'vi' and 'emacs', which are likely nothing like what you have encountered before - everything is command driven rather than using the mouse.
There are plenty of more basic (and less intimidating) editors, but if you want to really get into the command line (more normally known as the 'shell' in UNIX/Linux), then you could do worse than to try one of them. There are religious wars over which is best - I'll try and be impartial in stating:
vi (or vim - Vi iMproved): Available on every UNIX platform in a basic installation. Very powerful once you get used to the syntax, which can be a bit obscure at times. Also very reliable, in 20 years of using it I don't recall one incident where its crashed.
emacs: Almost an operating system in its own right! More full featured than vi with more language support and plugins. If only I could ever work out how to quit from the damn thing...
Then just decide what you want to do, and with a bit of googling you should be able to get there.