The film, the Matrix is the 'stick' that prodded the brain matter of the masses to contemplate the ultimate contemplation. As such, the Matrix must be seen as a representation of a new archetype or story for our time. It erupts into our consciousness with some powerful themes. To not ask these questions, is itself the biggest danger. The Matrix suggests to us that the reality of the world as we know it is superior to the reality of the Matrix because there are certain elements of control within the Matrix that terminate freethinking individuals.
Control here is the operative word.
As with Terminator, The Matrix reflects our fear of technology as it creeps ever further into our lives. We can no more rid ourselves of technology now than we can rid ourselves of conscious thought. It's here to stay. Only with our technology can we possibly manage a biosphere with a population heading toward ten billion. At the same time that technology is merely an extension of us, it is the great freer of our time.