The Matrix is a film filled with religious and philosophical symbolism. The plot supposes that humans live in vats many years in the future, being fed false sensory information by a giant virtual reality computer (the Matrix). The perpetrators of this horror are machines of the future who use humans as a source of power. Humans are literally farmed.
The central character of the film, Neo, is presented to us in the opening part of the film as a loner who is searching for a mysterious character called Morpheus (named after the Greek god of dreams and sleep). He is also trying to discover the answer to the question "What is the Matrix?"
Morpheus contacts Neo just as the machines (posing as sinister 'agents') are trying to keep Neo from finding out any more. When Morpheus and Neo meet, Morpheus offers Neo two pills. The red pill will answer the question "what is the Matrix?" (by removing him from it) and the blue pill simply for life to carry on as before. As Neo reaches for the red pill Morpheus warns Neo "Remember, all I'm offering is the truth. Nothing more."
The film as a whole and especially the choosing scene is deeply compelling. Why is the choice between what you believe you know and an unknown 'real' truth so fascinating? How could a choice possibly be made? On the one hand everyone you love and everything that you have built you life upon. One the other the promise only of truth.
The question then is not about pills, but what they stand for in these circumstances. The question is asking us whether reality, truth, is worth pursuing. The blue pill will leave us as we are, in a life consisting of habit, of things we believe we know. We are comfortable, we do not need truth to live.
The blue pill symbolises commuting to work every day, or brushing your teeth.
The red pill is an unknown quantity. We are told that it can help us to find the truth. We don't know what that truth is, or even that the pill will help us to find it. The red pill symbolises risk, doubt and questioning. In order to answer the question, you can gamble your whole life and world on a reality you have never experienced.
However, in order to investigate which course of action to take we need to investigate why the choice is faced. Why should we even have to decide whether to pursue truth?
The answer in short, is inquisitiveness. Many people throughout human existence have questioned and enquired. Most of them have not been scientists or doctors or philosophers, but simply ordinary people asking 'what if?' or 'why?' Asking these questions ultimately leads us to a choice. Do you continue to ask and investigate, or do you stop and never ask again? This in essence, is the question posed to Neo in the film.