The Matrix is a simulated reality existing as an electronic construct in which the participants are connected electrically at neuronal level. As opposed to virtual reality, the participants are unaware of their existence outside of it. However, during their existence in the Matrix, there must be some type of brain activity.
The types of brainwaves are Alpha, Beta, Delta, and Theta. Alpha and Beta occur during wakefulness, Delta during deep dreamless sleep. Theta are those waves occurring during meditation and dreaming, and are related to the neo-cortex and hippocampus, which plays an important part in the conversion of short to long term memory and spatial coordination.
The only type of brainwave that could possibly be seen while a subject is in the In-Universe would have to be Theta, and so similar to the dream state.
The people in the Matrix are unaware that they are not living in “reality”. When Morpheus offers Neo the pills, he is offering a decision to remain in the dream, or to lucidly choose to wake up when the dream turns unfavorable, such as adepts of lucid dreaming are able to do.
The Red Pill is a metaphor, similar to the lucid dreaming technique of using the spinning top as depicted in “Inception”. Practitioners of lucid dreaming claim that they can control the direction of their dreams, and choose to awake when they want.
The act of choosing the red pill symbolizes that decision, causing him to awake. His first reaction upon awakening is to yank the feeding tube from his throat, creating a feedback loop. His disconnection from the neural probe provokes an automated disconnection and ejection.