I've been complaining about the rise African-American fiction sections since I worked at a Borders back in 2005. As Carleen Brice points out, there are actually two problems with the sections: the first is that they tend to send a signal to non-black audiences that These Mysterious Books Are Not For You, the second is that they lump together a wide variety of books under the broad genre of "African American fiction", most of which have nothing to do with each other.
The African American fiction section attempts to deal with the complaint that African American-authored books are difficult to find. However, the reason African American books were so difficult to find is because they were and are marketed in a different and often lesser manner than "mainstream" fiction, and usually in a way that makes any black author fit either into the Maya Angelou/Toni Morrison "Soul of Blackness" mold or the Everyone Else "Literary Soul Plane" mold. If the problem with African American-authored fiction was that it was on fire, the African-American section is a hastily-constructed fireplace. At least it's got some classy kente cloth bunting, though.
It's a nice Catch-22: nobody but the people we market to buy these books, so there's no reason to market them to anyone else. This leads to black authors inevitably tailoring themselves - or having their books tailored - to the perceived African American niche market, which, because it's large enough to remain predictably and comfortably successful for the good authors who enter it, provides no impulse for publishers to find a different or more expansive way to market them.
The solution is simple, which means it's equally unlikely that it'll ever be followed: publishers and booksellers can pick out good, mainstream novels penned by African Americans and market them the same way they would the same book by a white author. If James Patterson can write eight million terrible bestselling mysteries about a black protagonist, then actual black people can probably write equally terrible bestsellers about equally unbelievable black (or even white!) people. Just give us a chance!