The students and professors at the black college dislike Trueblood because he is a threat to them. Since its founding, the college has supposedly been an opportunity for black people to break out of the societal binds that hold them down. Whether this potential freedom is real or not is debatable, since the professors and students alike seem extremely beholden to the white benefactors.
What Trueblood represents is a legitimacy to the negative stereotypes that the people at the college are trying to break and overcome. He justifies the white man's oppression. If the founders or learn his story, they can use him to validate their superiority, even though he is not typical. His "accidental" sexual encounter with his daughter and the fact that both his wife and daughter are pregnant by him makes him both the pariah of the black college community and the prophet of the racist white community. The black leaders try to rid themselves of him send him away, but the white leaders treat him better after he impregnates his daughter and give him clothes and more money than he had ever had.
One of the major themes of Invisible Man is IDENTITY. Even his name is symbolic. True blood implies that he is the embodiment, at least in the eyes of the whites, of what people of African-American blood really are. Trueblood establishes an identity for the college that they do not want. He identifies blacks as people of low morals who lack self-control. The college is attempting to create an opposite identity for African Americans. The existence of Trueblood and people like his is an extreme threat to that hoped-for identity and acceptance.