Because nearly everyone gets it wrong.
First, her own explanation in 2008:
Do you regret referring to Bill Clinton as the first black President? --Justin Dews, Cambridge, Mass.
--People misunderstood that phrase. I was deploring the way in which President Clinton was being treated, vis-à-vis the sex scandal that was surrounding him. I said he was being treated like a black on the street, already guilty, already a perp. I have no idea what his real instincts are, in terms of race. (Emphasis mine).
http://www.huffingtonpost.com/2008/05/08/toni-morrison-on-calling_n_100761.html
The original from 1998:
http://ontology.buffalo.edu/smith/clinton/morrison.html
In a quite baffling and frustrating manner, it was not a "story" but a compilation of revelations and commentary which shied away from the meaning of its own material. In spite of myriad "titles" ("The President in Crisis"

, what the public has been given is dangerously close to a story of no story at all. One of the problems in locating it is the absence of a coherent sphere of enunciation. There seems to be no appropriate language in which or platform of discourse from which to pursue it. This absence of clear language has imploded into a surfeit of contradictory languages. The parsing and equivocal terminology of law is laced with titillation. Raw comedy is spiked with Cotton Mather homilies. The precision of a coroner's vocabulary mocks passionate debates on morality. Radiant sermons are forced to dance with vile headlines. From deep within this conflagration of tony, occasionally insightful, arch, pompous, mournful, supercilious, generous, salivating verbalism, the single consistent sound to emerge is a howl of revulsion.
But revulsion against what? What is being violated, ruptured, defiled? The bedroom? The Oval Office? The voting booth? The fourth grade? Marriage vows? The flag? Whatever answer is given, underneath the national embarrassment churns a disquiet turned to dread and now anger.
African-American men seemed to understand it right away. Years ago, in the middle of the Whitewater investigation, one heard the first murmurs: white skin notwithstanding, this is our first black President. Blacker than any actual black person who could ever be elected in our children's lifetime. After all, Clinton displays almost every trope of blackness: single-parent household, born poor, working-class, saxophone-playing, McDonald's-and-junk-food-loving boy from Arkansas. And when virtually all the African-American Clinton appointees began, one by one, to disappear, when the President's body, his privacy, his unpoliced sexuality became the focus of the persecution, when he was metaphorically seized and bodysearched, who could gainsay these black men who knew whereof they spoke?
The message was clear "No matter how smart you are, how hard you work, how much coin you earn for us, we will put you in your place or put you out of the place you have somehow, albeit with our permission, achieved. You will be fired from your job, sent away in disgrace, and--who knows?--maybe sentenced and jailed to boot. In short, unless you do as we say (i.e., assimilate at once), your expletives belong to us." (Emphasis mine.)
While it is true that Clinton had huge support from the African American community, Morrison wasn't claiming that Clinton was the first black President based on his policies but rather, she was commenting on his victimization from the elite in DC and the consistent slap-downs directed towards his "uppity" self.