I just finished the Matrix Trilogy and there is one thing I feel confused about. My assumption is that the controller of the matrix, whatever it is, is aware that Neo is attempting to destroy it and free the people there, and is trying to stop him. If my assumption is correct, then why do he/she/they not simply cut the connection from outside after Neo's real body has been freed? There will be no way for any human outside the matrix to get in again, thus no way to talk to the keymaker. So why is the connection still open? Looks like this is a big security flaw in the matrix to let them in and out freely - well, almost freely.
As others have noted, The Outsiders actually 'hack' into the Matrix.
This is the core where we broadcast our pirate signal and hack into the Matrix - Morpheus
Assuming the Matrix runs in a similar fashion to our current level of technology (i.e. servers, ports, firewalls etc.) This would mean the towers of people-pods would need an open port/open connection in order to access the Matrix.
Obviously the people-pods are using wireless technology, because we witness some of them being detached and used to power other things by the squids and other 'farming' robots.
Which means it would be (reasonably) trivial for a ship to broadcast a signal that emulates that of a pod, connect a person up and have them walking around inside the Matrix in a matter of minutes.
As far as the machines trying to mitigate the damage caused by the outsiders hacking in, we see evidence of the robots trying to choke them- delay them from being able to connect. There is talk in the second movie about trying to find good areas to transmit the signal:
Morpheus: My apologies - to all; but as you are undoubtedly aware of it, it has become increasingly difficult to locate a secure broadcast position.
Vector: Squiddies got all over my best spots.
Ice: The main-lines are crawling with them.