I recently came across the following quote from Freud:
"Humanity has in the course of time had to endure from the hands of science two great outrages upon its naive self‑love. The first was when it realized that our earth was not the center of the universe…The second was when biological research robbed man of his peculiar privilege of having been specially created, and relegated him to a descent from the animal world…But man's craving for grandiosity is now suffering the third and most bitter blow from present‑day psychological research which is endeavoring to prove to the 'ego' of each one of us that he is not even master in his own house, but that he must remain content with the veriest scraps of information about what is going on unconsciously in his own mind…This is the kernel of the universal revolt against our science." (A General Introduction to Psychoanalysis, Eighteenth Lecture)
(Freud's conception of the psychoanalytic unconscious is not the one accepted by cognitive scientists today, and I don't know whether or not the above was truly at the root of criticism he faced. But, Freud was perhaps more right than he could have known about the third "outrage" to humanity's naive worldviews. Modern research on the cognitive unconscious in psychology and cognitive neuroscience has presented a wealth of evidence that picks away at the notion of a unified, directly-known, causal, conscious self.)
In any case, sort of sums things up, huh?