I think his history of participating in racially discriminatory housing practices, among some other things, has made the black community somewhat wary of him. There are also a lot of black Muslims in some cities, which may be an issue given his discussions of that religion. Not sure what Chicago's black Muslim population is like. Oh, and the KKK was pretty vocal about supporting him in the campaign. And he spent about 8 years questioning the legitimacy of the first black president.
Basically, a bunch of stuff kind of combines to make him not very palatable to many in the black community.