It seems, you didn't even read until the end of the article:
> Therefore, the most likely answer is that the distinctive shape of 1 World Trade Center is either trademarked (although I could not find it within USPTO databases) or is so recognizable that it is easily defensible via a common law trademark and the game developers were unable to secure a license to use the trademark before their deadline.
Fixed as per PinguTS: trademark law. D'oh.