Associating skyscrapers with New York doesn’t constitute approval for either.
You might truly abhor racial prejudice and still recognize that black people are usually portrayed in a negative light, and thus “blackness” and “bad” are associated in your mind. That’s not being prejudiced as such.
But building skyscrapers (and high-density cities more generally) is the most environmentally sustainable thing we can do. http://economix.blogs.nytimes.com/2009/03/10/the-lorax-was-wrong-skyscrapers-are-green/
Your main point, however, is right on.
Associating skyscrapers with New York doesn’t constitute approval for either.
You might truly abhor racial prejudice and still recognize that black people are usually portrayed in a negative light, and thus “blackness” and “bad” are associated in your mind. That’s not being prejudiced as such.