The idea of poking holes in official dogma is novel for the right, and so the reactionaries have adopted the "red pill" symbolism. This causes many to associate the two, especially those newly enamored with the concept after having seen through their first layer of the memetic prison.
That's fine. Just if later in life you come to a revelation that does make the term click for you, do yourself a favor and make sure you keep going with the questioning rather than taking your newly altered model as unassailable truth and thinking you're out.