Unconscious Revelations

Once upon a time, a writer got a critique in which her well-written protagonist was praised for being unique. This uniqueness took the form of being narcissistic and racist. The writer in question was surprised that readers perceived the character this way.
Another time, a writer created a protagonist who was brave and smart and deboniar--think a scientist version of James Bond. Basically, he could do anything from run a mass spectrometer to shoot a sniper rifle--and the women swooned over him.
In yet another example, a writer created an evil antagonist who ended up being the protagonist's father. And--wait for it--the next book the author wrote also had an evil father antagonist.

What do all these examples have in common? I believe the authors unconsciously revealed some aspects of their personality or paradigm. The 2nd author thinks he is like a scientist/James Bond. The 3rd author has a bad relationship with her father.

Is unconscious revelation bad? I'd say: no. As authors we have to use all the tools at our disposal, including our unconscious and our subconsious. In fact, in my experience, first novels often involve a lot of unconscious revelation.
I think this is another reason it's great to get feedback on your writing. If the reader thinks the protagonist has qualities the author didn't want him to have ==> change him! That's one of the beauties of being The Author, Great and Powerful. :)

Good luck with your conscious and unconscious revelations!
Hhm... Maybe I should go reread my first novel.