Those crazy guys at GameSpy have posted a Hacking Guide for Enter the Matrix. Being a big part of the game, the hacking system is very complex and can take a while to explore, so instead of tearing your hair out you can read the guide and become a Happy Hacker:
The hacking system in Enter The Matrix is in some ways similar to an old MS-DOS interface, with basic commands like DIR, etc. Once you've fully "hacked" the system, you can view movies, look at artwork from the game, get messages from some of the key characters from The Matrix, "drop" weapons for Ghost and Niobe to use in certain locations in the game, and even unlock a few new modes, including multiplayer fighting and mini-games.
To begin, select the Hacking option from the main menu, select a savegame to associate your progress with, and the interface will come up. After a brief "virus scan," the lower portion of the screen will show a command list and keyboard layout. If you're playing on a console, you'll be able to highlight many of the commands and execute them; if you're on a PC, it's a little easier to do the typing, but you can also quick-execute commands using the CTRL key (NOT Enter). Since the hacking "campaign" is fairly linear, we'll run through it drive-by-drive.