Most companies aren't taken to court by governments across the world for anti-trust and monopolisitic behaviour, so no, "haters gonna hate" is not a sufficient explanation for their reputation. Most people do not begrudge success.
Apple might well pick up a negative reputation for their continued abuse of the patent system, and again, its not just because they're big, it's because they're using unfair methods of competition.
"Haters gonna hate" is not what I was going for. You were talking about public perception of companies and their poor business practices. I think we agreed that virtually all public corporations are guilty of some form of shady business. What I'm merely stating is that the perception of their wrongdoings is generally proportional to how big the company is and how well known their company is.
For instance, when Apple was just releasing the iPod and their other new products under Steve Jobs, it's not like they weren't using Foxconn to build them. But did anyone care, was there ever a single story about it? No. Now that Apple is bigger than Microsoft, those negative stories abound.
So, using some amorphous metric like "more negative public perception" doesn't really objectively measure anything and moreover isn't something that can even be proven. Something that would be better is some objective measure like consumer complaints per million costumers or some sort of customer satisfaction metric taken by some third party.