Right after the white creature was ripped out of his stomach he was in disbelief of the sight of it.
Neo exasperatedly asked "so that thing was real?" Before Neo is able to discover his reality Morpheus questions him.
"Have you ever had a dream, Neo, that you were so sure was real?" and he continues, "What if you were unable to wake from that dream, Neo? How would you know the difference between the dream world and the real world?" In the movie the dream that Neo awoke to was actually his own life.
In Descartes eyes the way in which humans can justify knowledge is from a few simple principles of Euclidian Geometry.
Euclidian Geometry begins on the fundamental axioms which are self evident and irrefutable.
Then by using simple deductive principles the person can build on that knowledge by deducing the rest of their beliefs.
So Descartes is really trying to find an absolute certainty about the nature of everything.
Neo is on a very similar quest.
When Morpheus presented Neo with two options, Neo chose the pill of understanding.
Descartes also tried to lay down a completely new foundation of knowledge in search of the truth.
Morpheus tells Neo that he is a slave to his own mind.
Everything that he knows is false because an artificially intelligent computer system called the Matrix controls everyone's personal reality.
Before Neo was able to break out of the Matrix his life was not as it seemed.
Everything he knew was false.