If you write code day in day out you SHOULD be comfortable on the command-line. That's why I highlighted in the article that I need two tools to do my development: an editor and version control. You use these tools every day--EVERY day. There's no excuse for not knowing them intimately. They are the foundation for doing your job.
GUIs also aren't always available across platforms, either. For the most part, all the git CLI commands port from Mac, Linux and Windows (msysgit). Also, have you ever tried using a GUI when SSH'd into a remote server in a pinch? You can't. And you'll really wish you invested the time to learn those underlying CLI commands.