The Matrix was the computer programmers idea of the universe. No computers, no Matrix universe!
I think the Matrix had something to do with the nature of reality, or what is reality. A reality constructed soley by the philosophy of computer hackers and programers. It was a concept already explored by Plato, De Cartes, and Kierkengaard that there is more to life than what is seen.
I found the Matrix to be merely entertaining, but not profound. It was not my generation movie, I couldn’t identify with all the leather costumes, the blatant defiance of authority, the technocratic hubris, and punk rock mentality.
I still prefer 2001: A Space Odyssey (which I saw in 1968, and that was very profound) and the Hitch Hikers Guide to the Galaxy (42).