No that's exactly what he said.
Here's a post from another board that explains it pretty well.
Neo is not in a coma. He is still conected to the matrix. well matrix #2. Trinitry and the rest are in the matrix #1
If you listen to the architect he said there was a slim few who could not accept any matrix. They had to fight for freedom no matter what. Well the real world is matrix #1. Its a sublevel for the .001% who fight.
when the sentinels are coming, neo stops them realizing he is part of the .001% who fights and he is in a differnent matrix so he uses his powers.
what the directors meant to do, is basically forshadow what is to come from matrix 3, that is when people will realize that zion is actually a component of the matrix, not of the real world
The the oracle asked neo in matrix 1, do you believe in fate, neo said no, and believed he is in control of what his future will be, which basically means non of them are actually free, hence the ability for agent smith to shift matrices, they never left the matrix, and in this point in time they are about to realize that they are still part of the program
My question now is I am begining to think that neo himself is just another program, doing his job... Makes you think.