"I think therefore I am." I think, therefore I exist. I guess that is true for all the people who live in the Matrix because they still have their conscious will. But the manner of existence is important here. If one never realizes that he or she is living in virtual reality and that they are actually like plants in a greenhouse, does that count as existing?
The movie brings out a brilliant question, what is reality? If reality is simply people feeling things and having emotions then a machine can simulate that by stimulating the neurons in our brain.
This is exactly what Aldous Huxley wrote in his masterpiece "Brave New World", where people gave up hope and courage, and even complex emotions. They opted for eternal, drug-induced, fake happiness. What is happiness? One can never truly understand happiness unless he or she experiences the other side of happiness too. Just like you can't fully appreciate and understand the value of life unless you realize that one day death would come. However, the other side of happiness is sadness, disappointment, and rage. These things are considered harmful in the society that Huxley wrote and are therefore avoided. Ecstasy can be induced because our emotions are just neurons firing in our brain. But does ecstasy count as happiness? In a world where people gave up the courage to dream and to be disappointed, people can never truly experience happiness.
In the Matrix, people still have their free will and they still feel things. But you can already see that some of them refuse to believe that their world is virtual reality. They refuse to doubt, to question, to risk having the meaning of their life taken away. After all, what's the meaning of your life if you live in virtual reality? Helping others won't work because you're helping simulations. Saving the world doesn't matter because the world is virtual.
The question comes, which is better, to live in a safe, controlled virtual reality, or a dangerous and mostly disappointing real world? The society in Aldous Huxley's book made a choice. They chose the former option. I think pretty soon we'd have to consider that question too.
The movie is eventually about courage, the courage to see the real world with your own eyes, to acknowledge all the good things and bad things that come with it too. Some people don't have that courage. They don't want the negative emotions, the pain, and the suffering. But happiness is only real when being compared with suffering and pain. In a world without disappointment, there is no dream and hope either. In a world without pain and suffering, there is no true happiness either.