Apu was one of my favorite characters, and next to the rest of Springfield I wouldn't say he was portrayed as any kind of bad guy. But I think it's entirely fair to find fault with him and the stereotypes used.

The "This is why we can't have nice things" guys are the ones who use this type of character to mock people of Indian descent. Having heard about their experiences, I would say that the bare minimum that should be done is involve someone from the community you're portraying, when creating a character who stands out as someone of that community.