I'm skeptical that people who've taken a long time to accept that Quirrel is Voldemort constitute a significant proportion of HPMoR readers. Sure, I've noticed a considerable number of them too, but HPMoR has a lot of readers. There's a risk of availability bias here; a reader who expresses skepticism that Quirrel is Voldemort automatically attracts attention from anyone who thinks it's obvious, whereas other people who think it's obvious don't.

Personally, I've had no trouble at all accepting that Quirrell is evil ever since his first class, where he praised Harry's killing instinct. Villains pointing out and encouraging protagonists' darker impulses is a time honored trope, and praising an eleven year old in front of a whole class of other children for his drive to kill seems pretty indicative of evil to me.