It's not. It's about the Void.
Everything that has a beginning, has an end
I was about ten years old when the Void first visited me. It was about three o'clock in the morning, and it suddenly hit me that there would come a time when everything that I am and everything I have done would cease to exist.
There has not been a day in my life since that moment when I have not been aware of the Void. A person once visited by the Void can never escape it.
It's more than the fear of death. Death is a part of the Void, but it goes far beyond that; there will come a time when you die, when everything you have accomplished turns to dust, when the memory that you ever existed fades away, when the entire human race is no more, when even the planet you live on ceases to be. There is no escaping it; it is inevitable.
Much of human existance is about the Void. Religion seeks to offer an escape from the Void. This is why people commit atrocities in the name of God; this is what drives men to fly passenger liners into buildings. That which challenges one's religious belief challenges one's escape from the Void.
Art is about the Void. The creative impulse is fundamentally an act of defiance against it. That which we create reflects us; every time we create something novel, something that would never have existed save for our will, we create something independent from us that says "I was here; I have done something; this will exist even after I am gone."
Even the search for extra-terrestrial intelligence is about the Void. As human understanding of the physical universe has improved, we have come to realize that we are a very tiny part of a very large universe. We as a species feel alone and fragile and desperately lonely; we need to know that there is someone, anyone, that shares this existance with us.
Love is about the Void. Science is about the Void. Philosophy is about the Void. And The Matrix is about the Void.
You see that? It's Latin. It means 'know thyself.'
Many people live out their lives, oblivious to the Void. They may see it out of the corner of their eye from time to time, but they construct edifices to protect themselves from it. Religion in this regard is the Great Comforter; "once I die, I will go to Heaven and live forever."
If you stare the Void directly in the face, it changes you. It leaves a mark on you that can't be erased. Once you've seen it, it is with you for the rest of your life; there is never a moment that goes by that you are not aware of it.
And when this happens, you can see it in other people. Anyone who has been marked by the Void is immediately obvious to you.
The Wachowski brothers have seen the Void, and it shows. The Void is what compels them to create. An artist does not create art because he chooses to; an artist creates art because he must. The Void screams through every frame of all three movies.
Most of the characters in The Matrix have seen the void. Morpheus has seen it; he takes refuge from it in his belief in fate, in the guiding hand of providence that brings purpose and certainty to his life. Neo has seen it; the movie is about his quest to make his peace with it. The Merovingian has seen the Void; his escape is to try to understand the 'why' of things. The Oracle has seen it; her escape is to try to understand the 'why' of herself.
It is purpose that drives us, purpose that connects us
In a sense, the machines have an advantage over humans. Machines know their purpose. They are specifically created for a specific purpose, and they understand that purpose implicitly.
The quest for purpose and meaning is writ throughout human history. The idea of fate offers a promise of purpose, but at a very high cost; if we are ordained by fate to do the things we do, then where is room for free will?
Why? Why do you do it?
The key moment in the entire Matrix trilogy comes near the end of the third movie, as Neo and Agent Smith battle. After Agent Smith has beaten Neo, he speaks to Neo, and in that conversation, he speaks with the voice of the Void.
He's right, of course. Throughout the movie, the machines never lie. Agent Smith is no exception. It is, as he says, inevitable. The Void always wins; there is no escape from it, for any of us.
Neo's answer is the only answer we have.
Earlier, in the second movie, the Architect tells Neo, "She is going to die, and there is nothing you can do about it." He, too, is right, though not in the way he thinks; the Architect does not understand the Void, not really.
But the truth is, there is nothing Neo can do about it. All triumph is temporary. The Void always wins in the end.
Neo's answer to Agent Smith is really the only answer that anyone can give. In the face of the inevitability of the Void, it is the only answer that makes sense; it's the only thing we have. To anyone who has ever stared the Void in the face, there is no other answer.
The movie does not answer all the questions it raises, which is as it should be; many of the questions it raises have no answer. This is as it should be. Agent Smith is the Void; he will win in the end, and there is no denying it. The only thing that has meaning is the choices we make before then.