The red pill is largely a reference to
psychedelics in a scene from the movie "The Matrix". In that scene Morpheus says:
"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."
Psychedelics, when properly used, help break down social constructs of the world and help people see it for what it really is. This is illustrated in the scene when Neo takes
the red pill and he begins to hallucinate in a manner consistent with psychedelics. Soon he wakes up, and for the first time, sees the real world around him. He realizes that since birth he was actually living confined in a small life-sustaining pod among millions of other pods, in what is basically a farm for people created by and run by machines. This imagery parallels our reality as many come to realize, whether through psychedelics or other means, the dogma of everyday life, the lack of individuality, and realize how much control and influence society has over our lives.
(Note: Some recently, as of 2020, have falsely interpreted "the red pill" to be a reference to The Republican Party of the Unites States since that party is often represented by the color red. However, the term "the red pill" was commonly used in association with The Matrix long before, since 1999, when The Matrix was released.)