EY and Quirrell couldn't have spelled it out more clearly.
Shouldn't this have occurred to Harry as well? When does he make the connection to that discussion?
Harry has repeatedly shown that he's blind to Quirrell's darker motives. It seems to be a necessary contrivance: if he turned against Quirrell before he came fully into his power, he'd lose. I can think of a fictional justification for it, though. He applies the same rationalization to Quirrell's actions that we use when explaining our own, and he does it because he's a copy of the person he's making excuses for. It's probably not psychologically realistic, but it's neat enough that I could suspend my disbelief if it turned out to be the case.
All sorts of biases are at work in Harry towards Quirrell. Halo effect from his power, knowledge, competence, and rationality. Gratitude for saving Harry's life. For helping against the bullies. For sharing the outerspace spell.
Respect for Q because he seems to respect Harry, and plays to his vanity. The Uber Competent adult mentor takes him seriously and tells him he is destined for great things, and includes in his plotting and actions. He's the Dad Harry has always wanted.
Besides Hermione, he's the only friend Harry has ever had. He didn't quit in Azk...
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: