I believe that the Linux community must come to terms with the fact that their products must address the issues you point out.
Sadly, the approach of stating, or at least implying strongly, that the average “windoze” users aren't as smart as Linux users remains prevalent.
I hope that the Linux community can find their way past this problem eventually. Watching the evolution of Linux over the years, I think that some of the developers are beginning to “get it”, but it will still take a while.
I enjoy driving a stick-shift vehicle. It's fun to manually control the acceleration, deceleration, torque curve, etc., but my wife (who has, and can drive one) is only interested in owning an automatic. Why? Because she sees the vehicle as simply a means to an end (i.e., getting from here to there without giving any thought to the vehicle).
I could spend a lot of time repeating how much more control over the vehicle she could have, how much more enjoyable it would be, etc. But that would only be received by her as smug and irritating, and it certainly wouldn't change her mind.
I think that Linux devotees continuing to “talk down” to users of windows (or other GUI-faced programs), will only come across as smug and condescending.
I don't think “command line” inputs are ever going to overcome GUI clicking for the average PC user.
People should stick with the system they like and that works for them.
This article was not meant as a way of saying everyone should switch to Linux. It was meant as a caveat to those who are considering the switch that there is more to it than merely popping in a disk and then doing the same things they've always done.