It's a double edged sword - the more intuitive the software becomes the further users distance themselves from understanding how said applications work. And when something goes wrong, the user will usually be unable to fix the problem themselves.

Take older Windows OS's for instance. The user experience can't compare to the new Mac OS or Windows 8 but the user was more involved in how things worked and had more access to the internal controls. Having the user involved made the user more savvy about how the system worked.