Holden is alienated from the world around him because he is unable to integrate himself within it. From the opening passage of the book, Holden demonstrates an inability to be a part of the world around him. Whether he does this because he feels uncomfortable with this world or he believes he is better than the world around him is not as important as the fact that he cannot participate in this world. Holden's fundamental mistrust of people and his detest for authority figures create a potent combination that makes Holden alienated from the world.
Certainly, this is the case at Pencey Prep, but it is also the case in New York, where Holden feels fundamentally different from everyone else. Essentially, until he meets up with Phoebe, Holden feels incapable of being a part of any social unity. The fabric of society does not include Holden's voice. He does not seek to be validated by this world and it does not seek to authenticate his own experience. It is for this reason that Holden ends up being alienated from the world around him. His separation from this world is what defines him, for better or for worse. In the final analysis, it is the fact that he simply does not fit into any part of the world around him that he is estranged from it.