That is the issue, and why Linux has not yet become a major force on the desktop. Too many times stuff will go wrong and it is down to a command line to fix it. Too much configuration exists within the command line there is no graphical user interface for it. There is no single Linux version, so stuff is stored all over the place. There is not a single package manager (Do I need the .deb, or the .rpm?).
This is what confuses users, and the choice paralyses them.
I am a geek, I absolutely love playing with different OS's and whatnot, but I am sick and tired of having to worry that updating is going to cause my OS to not boot (I'm looking at you Ubuntu and your nouveau graphics driver).
Linux package managers may have "solved" the problem, but that is not what you get points for. You get points for getting users to adopt it and use it. Apple gets an A in that category (App Store on Mac OS X and iOS is a success), Linux a D (Package managers are a success, but the user experience isn't).