I'm probably missing an tag, but consider the evidence.
Quirrell's "they have tolerated worse in their hallways" and give a finger from my wand hand, suggest that bullying has been tolerated for a long time.
What are Snape's adult motives and goals? How much of a panopticon is Hogwarts or House Slytherin there? When he tasked 7th-year Rianne Felthorne, presumably with sending the message back via Bullstrode, she lost count of the charms cast and didn't show recognition of them. Harry would have recognized them from Bester and Quirrell. Hogwarts is a centre of power, perhaps funds his Potions research and precautions againts Voldemort's return. Is conditioning Hogwarts students to fear him defending his future position or building a power base.
Are Dumbledore & Snape treating Quirrell as a bird in the hand, under close observation - Bellatrix's escape is still under investigation after all. Who set up the ambush outside the library? Snape or Quirrell? 2PM is too early for Harry's Time-Turner unless the shield was circumvented. Was testing for The cloak of Invisibility a hint from Snape?
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
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. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
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: