I don't think Twain is politically incorrect, or widely viewed as
such by those who are familiar with his work. Twain consistently shows
an extremely modern, humanistic view of African-Americans, Jews, and
Asians that shows he thought deeply about these issues and stands up well
today. Twain's views on American Indians do not stand up as well, but
those do not make up a large part of his work.
I suspect that the problem in schools is the very complexity
Twain brings to the subject. Racial topics have become so charged that
teachers are reluctant to express their own views or to talk about race
in any depth. Twain's popularity naturally is not helped by his use of
the word "nigger," then in wide use but now highly offensive.
John M. Baker