I suspect that there are a multitude of reasons why INTJs are treated negatively. For example, INTJs are a bit of an Internet meme at this point, which consequently means that their portrait to the uneducated is of the exemplary traits hyperbolized, often in a negative light. Those who lack skepticism, or just don't care to know better, will hold this stereotypical image in their mind and will judge INTJs with it. Also, it's easier to judge people by their affiliated group than by their merit, so those who, again, don't care to learn about the type or just want to get someone's knickers in a twist will go on making ungrounded assumptions and accusations. This general hate is through emotional thinking that lacks any maturity or rationale.
That's one reason I could think up of, anyways. There's also people scapegoating, being too lazy to analyze someone individually ("This person must be an INTJ, that's how they all act!"), etc, etc. Not very respectable actions in my eyes, and clearly not in other's either.