Carruthers
You either need to define your terms, or stop making sweeping generalisations. "Pilot Error" (or human factors as we call it these days) can include just about anything. You could justfiably say that Sept 11 was "pilot error" if you wanted to (in the sense that they made an error in allowing access to the flight deck).
All that automation will do is create a new class of error. You could call this "engineer error" (as in software engineer).
You also need to get out a bit and actually talk to some pilots and development engineers. The truth is that the technologies you mention are not intended to get the pilot out of the loop, rather they are intended to get the pilot further into the loop- by providing him with more and/or better information, and relieving him of some tasks that allow him to better monitor and manage the flight.
The "cock ups" you mention are more down to the fact that training is designed to allow pilots to safely explore their, and their aircrafts, limits- so that the same errors won't be repeated in real life. We call this "learning" and it isn't a sign of pilots being unable to handle their aircraft properly, or not understanding their systems.
In the end, the pilot is there to not only achieve a safe routine operation, but to cope with the (rare) situations that automation couldn't resolve. Any experienced pilot will tell you about those...