The human psyche is easily made comfortable with bad results if they don't appear to originate in human evil. Even when, as you correctly point out, it actually does.
JOKER: You know what I am? I'm a dog chasing cars. I wouldn't know what to do with one if I caught it! I just do things. The mob has plans. The cops have plans. Gordon's got plans. Y'know they're schemers. Schemers trying to control their little worlds. I try to show the schemers how pathetic their attempts to control things really are. So when I say that you and your girlfriend was nothing personal, you know I'm telling the truth. It's the schemers that put you where you are. You were a schemer, you had plans, and, uh, look where that got you.
I just did what I do best. I took your little plan, and I turned it on itself. Look what I did to this city with a few drums of gas and a couple of bullets, hmm? You know what I noticed? Nobody panics when things go according to plan. Even when the plan is horrifying. If tomorrow I told the press that, like, a gang-banger would get shot, or a truckload of soldiers will be blown up, nobody panics. Because it's all part of the plan. But when I say that one little old mayor will die, well then everybody loses their minds!
The flu was an act of God, and people easily moved on, unlike the other deaths mentioned there.