Something I don't quite understand about the anger towards Apu from some members of the Indian community (it's important to not be monolithic in these discussions, as not everyone who's Indian or Indian American is even offended by Apu, and that doesn't necessarily mean they hate themselves either) is that the anger is mostly directed at Hank Azeria and the showrunners, and the volatile degree of that anger.
Now is it a bit cringey that a guy who's not Indian is doing such a stereotypical accent? Sure. It's just a fact that a lot of how that character was intended to be funny DID stem from the premise of "lololol, silly indian accent, lolololo". But was it done out of malice or hate and not the same gentle mockery and stereotyping that went into literally every character on the show? Is there evidence of this? If not, why does Hari literally think about beating him down (which was intended as the cathartic punchline at the end of the documentary, and also something he's spoken about years earlier)?
Because if your main issue is that you were stereotyped and bullied IRL because of Apu, isn't the problem more because of the type of dumb Americans the Simpsons probably made fun of the most who assumed a cartoon was a substitute for reading literature and having cultural experiences and thought Apu was an accurate representation of indian culture?
And of course there's also the problem of representation in the media (especially at the time) which fuels ignorance, so I guess that's why so much of the anger is directed at Hank and the showrunners? Because they didn't challenge the status quo more? Ok, understandable. And the anecdote about the guy who guest voiced Apu's nephew pitching that character arch and getting turned down by the showruners confirms this. So then my confusion at this point is...why so MUCH anger?
Look, I have been beaten up over thirty times growing up for not being straight and standing out too much among the standard generic dudebro. To the point where I had to dress and behave differently to avoid being assaulted (which I was able to break away from in coleege). I know what it's like to be bullied and reduced, even if it's for different reasons. There are times even now where I feel some aggression rising due to all the times I was humiliated, singled out, attacked, etc.
But even after all that, it never got to a point where I wanted to beat up TV show runners for not educating the masses better on anti-conformity and inclusiveness. Inmy opinion, Hari in particular seems like he lets things get to him more than they probably should (his bit about raging over microsoft spell check putting a red squiggle under his name, and the bit about white chocolate being racist because it's not brown come to mind).
But my reaction to all that is still empathy, because clearly this stuff really gets to him, and that can't be denied. I don't get the level of anger, but then again, I've never been undermined on a large scale due to widespread ignorance of my culture. I don't know much about experiences he had now and growing up that shaped his emotions and psyche like that (which also seems to be shared by several in the indian community). For all I know, some truly horrific things which he hasn't disclosed, something far worse than microagressions, stereotyping and ignorance, happened to him to cause those feelings. Even if it's difficult for me to understand how a cartoon character that isn't a creation of malice could cause so much resentment, I feel for what he's going through and realize there might be something I'm not be seeing that puts that reaction into perspective more. You can't just reach easy conclusions about why someone you don't personally know feels the way they do. Some things are clearly right and wrong, but for the most part reality and human beings are far more complex than that.
Only other thing I'll add on this topic is I think Matt Groening's response linked in OP is fairly reasoned. So why didn't he say that as his initial reaction to the Apu doc instead of tweeting "People just looking to be offended, lololo"?