Man, I hate that I know this one. The scene where neo walks up and scares cypher? He's working on an auto-jack script to manage operator duties and building an escape plan. Before he turns off the screens there's also blueprints for the building where the group is later ambushed displayed, further implying he was plotting at that moment.

Edit - Operators are for when shit hits the fan to run support and adapt to the situation. The act of loading people in and out can be automated as long as there's no crazy variables to account for, like agents crashing the party.