Man vs Machine
The Matrix is a movie based on how machines have taken over and the resistance is fighting them. What is interesting is how the movie portrays humans and their machine-like tendencies. Not only do we see machine like actions in the humans, but there is also an abundance of human like qualities in the machines. In several scenes, we see how the actors are consistent in their actions in a nearly robot like manner.
Free will dilemma
In the movie, there is a discussion on whether humans actually want free will. This film shows this in how people are given a choice to pick the red or blue pill - each symbolizing free will or living a life that is comfortable but fake. They have the choice of a comfortable world or a free one that is real with all of its unpleasantries.
The mind and the senses
One final significant theme involves the issues of trusting your senses and objective truths. The objective truth is that everyone is trapped in the matrix, showing that everyone subjective view might be compromised. Neo learns in the movie that his senses might betray him and things are not always as they seem, making him more critical of his own and other people's views.