Well, I think the best way is study using the oficial documentation, Oracle Concepts, may be a good option for start, but if you want trainings, usually the oficials will show you a few of the both things (GUI or EM and command line).
Well, the good thing about CLI is that the way it works, is always the same. Which at the same time is a major reason why GUI's are harder to learn, since everything seems to work differently.
So, if you know what a command is, what a parameter is, how parameters are used, what a variable is, that's already halfway there.
There seems to be lots of videos on Youtube, about database backup/recovery, all using RMAN, which is a pure CLI.
To manage a database via Linux/Unix command line, means to manage a database through SQLPLUS, another CLI tool.
I would even be tempted to say you can manage a complete database using OS command line and SQLPLUS only. But, that would exclude the monitoring of Enterprise Manager, and the performance monitoring via the same tool.
Though CLI is the real-deal but the issue, now the emphasis on EM is way too much. So in the answer for your question, it's a NO. There isn't any course which is targeted towards only the CLI but on the contrary, it is the other way around. But it's not hard to know the CLI commands as there is Reference guide and the Administrator guide gives a lot of detail as well. Now, that said, I shall say that ignoring EM completely , at this moment-2014, wouldn't be a very wise decision. EM has grown much larger than just being a nice , monitoring tool . There are just a lot of features included in it now , for example, you can't even possibly imagine to manage the Exdata kind of machine just by CLI and so is multiple clusters, standbys, storage systems and the list goes on.So do keep looking at EM and playing with it. There are features now which would take minutes using EM but probably much longer if done using CLI.
The best training is to install everything on your own workstation, and play around and see how things work.
Anything you see on the internet is just a starting point.
The real learning is doing yourself.
The GUI vs command line argument is pretty simple.
GUI - good for performing many unique and simple tasks.
command line - best for automation of routine and complex tasks. eg backup.
It seems that the "OCA Oracle Database 11g: Database Administration I: A Real-World Certification Guide by Steve Ries, published by Packt Publishing has command-line (SQLPlus and SQL Developer) examples rather than Oracle Enterprise Manager examples. Other Certification Guides for the 1Z0-052 exam might be similar.
Hemant K Chitale
Even if you use the 2-Day guides, which are heavily slanted towards EM, you can still learn a lot. Before commiting a change in EM, there is often a button named "Show SQL". All Enterprise Manager is doing behind the scenes is executing a SQL statement on your behalf. Look a the SQL statement that EM will be executing. You can execute it in SQL*Plus, on the CLI instead. Go back to EM and make a minor change to the task at hand and see how the SQL statement changed.