This may be true, but for desktop computers? Not a chance in hell. Windows dominates by a looooong shot. A PC interface is where you'll be doing your command line stuff, not a phone, so you can toss all the Android/iOS devices out the window. There are very few PCs in the world that will need the command line, and even fewer people that would be skilled at it.
The only people out there using the command line are the diehard Linux users or if your job depends on it. Nobody on OSX is using the terminal, so that cuts even further into the Unix crowd. I would certainly agree that Linux users have a better understanding of computers, but not for the reason you're suggesting. Would you say that those who drive stick have a comparable understanding of their vehicle? Didn't think so.
The argument here is that you can drive your car the hard way or the easy way. It doesn't matter which you do because the end result is the same. For computers, you can open up explorer by firing up the ol' command prompt and typing "explorer ." or you can simply click the button on your taskbar. Knowing how to do the former doesn't make you any better at opening up explorer; the end result is the same.
Linux users have a better understanding of computers because they go much more in depth, not because they do comparable tasks with the CL that a normal computer-user would do. There is nothing "more in depth" that a manual driver can do that an automatic driver can't. At least nothing that isn't obsolete.