You may have read my breakdown of the original Matrix movie and how atheistic overtones/themes could easily be interpreted there. I noticed something else watching the movie the other night for the 158th time.
Morpheus, known in mythology as the god of dreams but ironically is the one charged with waking people up from the matrix, has an interesting exchange with Neo the first time they meet.
Like so many people who start to have doubts about religion, Neo has been looking for answers, too, because things just aren't making sense to him. In the following exchange pulled directly from the movie, I will substitute "the matrix" with "RELIGION" and you'll see the conversation still makes sense and holds up quite nicely as if Neo was an indoctrinated believer on the cusp of deconverting.
MORPHEUS: "Let me tell you why you're here. You're here because you know something. What you know you can't explain. But you feel it. You've felt it your entire life. That there's something wrong with the world. You don't know what it is, but it's there. Like a splinter in your mind, driving you mad. It is this feeling that has brought you to me. Do you know what I'm talking about?"
MORPHEUS: "Do you want to know what it is?
MORPHEUS: "RELIGION is everywhere. It is all around us. Even now, in this very room. You can see it when you look out your window or when you turn on your television. You can feel it when you go to work, when you go to church, when you pay your taxes. It is the world that has been pulled over your eyes to blind you from the truth."
NEO: "What truth?"
MORPHEUS: "That you are a slave, Neo. Like everyone else you were born into bondage, born into a prison that you cannot smell or taste or touch. A prison for your mind. Unfortunately, no one can be told what RELIGION is. You have to see it for yourself. ... This is your last chance. After this, there is no turning back. ... You take the blue pill. The story ends. You wake up in your bed and believe…whatever you want to believe. ... You take the red pill. You stay in Wonderland and I show you how deep the rabbit hole goes. ... Remember, all I'm offering is the truth. Nothing more."
You see, Morpheus, with the blue pill, is offering a chance to go back into oblivion, to return to a world where ignorance is bliss, even though the machines are using Neo's very life to extend theirs. The blue pill could also be symbolism as the believer pill (B for blue, B for believer) and the red pill could be a symbol for rational thought or reality (R for red, R for rational or reality).
It's just a thought.