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The "X" is there to stand for all the things we want to hide. (Remember the X-files). It has nothing to do with Malcolm X but the X in Malcolm X is also to hide something. The last name of Malcolm X was a white man last name and he wanted to hide it.
I disagree with your statement about what the X stands for in the title of the movie as well as the X-files and Malcolm X. X stands for the unknown. In the Autobiography of Malcolm X he explains that since he was given a white man's name he never knew his real last name. hence he changed it to X to symbolize the unknown. also the x files are called the x files because they are reports on the unknown behavior of the paranormal and supernatural.
Maybe the "X" has something to do with the graphical ressemblance with a swastika symbol, as well.
As a college student, I see this often. When the university starts a class and it is still in the experimental stage, it is given a course number followed by an X.... for instance, CompSci403X. The X indicates that it is a new course and that changes are still being made. I think that Sweeney was thinking of this method when he named Danny's class "American History X". Danny's class was new, experimental, individualized, and certainly not a part of his original curriculum.