You're wrong, and here's why. Neo only has any real power inside the Matrix and Superman is not jacked in, so he wouldn't be fighting Neo in the Matrix. Outside the Matrix, it would only take about 31 seconds for Superman to kicks Neo's butt. Neo can stop robots outside the Matrix, but that wouldn't do him any good against old Superman. Now I guess the other point would be that everyone is jacked in, most people just don't know it. With that argument, Superman would still win because he is much more powerful than Neo, and contrary to your statement, Superman actually does know how to fight, even without his powers. Neo's fighting ability is very much a part of his powers also, so you can't say he is so much better than my boy Superman on that one. Outside the Matrix, his fighting skills, speed, agility, and strength are all that of an average human. He couldn't beat Superman in or out of the Matrix. The only chance he would have of course is if he had a piece of kryptonite.
The point that I guess I overlooked is that the only way they could fight is outside of the Matrix, becuase of how hard Superman's skin is. They couldn't put all the implants in that would be needed for him to jack in to the Matrix. Therefore, they would have to fight in the real world. Therfore, Superman would win.
This is coming from a big fan of the Matrix by the way. I am just realistic and know that Superman would kick anyone's *** he went up against.