There are many GUI applications to deal with databases and with MySQL in particular. But for die hard command line enthusiasts, who grew up with Linux, the shell prompt is still prince.
You would be surprised at the vast amount of operations that you can do from the command line. Running commands on several databases at once, filtering users, getting detailed metadata, transferring data from the operating system to a database and the other way around, creating scripts from database data, creating SQL commands from database data.