After a certain point, i think every single web developer has to evolve to a point where you become well versed with the command line.

Whether you are on linux, unix, windows, android and everything in-between then it is essential to the craft.

You can sync and migrate thousands of files much faster using rsync or svn than ftp, as well as maintain better source control, migrate a large MySQL database in a few minutes vs another utility like PHPMyAdmin may take a long time or fail to do, creating and managing scheduled tasks with cron to name a few things.

There are options like Perl, which is a close relative of PHP so easier to learn. But there is also Bash Shell Scripting. So check out this tutorial from http://www.hypexr.org/ for more info getting started with bash. And if not Bash, Perl should be next on your list.