There is no spoon 
[sub]Tank, I need a duck and run program[/sub]
I think maybe the point is that human biengs in the real physical world have powerful energy resources within them that can be tapped. The humans trapped in The Matrix who think themselves ordinary and powerless over the world around them (like you and me) are suffering from “The [false] reality pulled over our eyes” to keep the population complaicent as they are tapped like Duracells.
Perhaps the changes Agents make in the Matrix in order to further their goals are not persistent, and at some point the room reverts back to the state which it was originally in before being meddled-with by Agents; the phone line is not permanently cut, that was only a temporary fix. A subroutine used for debugging purposes, then discarded.
To plunder, again, an already criminally-overused line (please accept my apologies): “Do you really think that successfully jacking out of the Matrix has anything to do with telephone wires, in this place?”
But then an even worse question arises: Why do they need telephones in the first place?
OK, bad idea. Move along, nothing to see here.
Damn! I hadn’t considered that! Very good idea.
There were a few early Matrix comic books released shortly after the original film which filled in some backstory. There was one where the agents confront a female computer programmer inside the Matrix who’s working on some AI software. They wanted her to finish it; apparently, the agents needed the humans to invent technology which they would then steal to improve themselves.