I searched all over the web, even read
The Ten Things You Can't Say in America, and I can't find a good rebuttal anywhere for the allegation that Wilson was a racist. Most
historians consider him a Great
President, and either refuse to tackle the issue or file it under his Pros and Cons.
James Loewen, professor of sociology at the University of Vermont, has written that Wilson "appointed southern whites to offices traditionally reserved for blacks" and "personally vetoed a clause on racial equality in the Covenant of the League of Nations."
The NAACP launched a public protest in 1913 against Wilson for "introducing segregation into the Federal Government."
He was, however, a deeply Christian person, and nearly every historian says that is what drove him to do all that they praised him for.
Sources:
http://www.cavalierdaily.com/.Archives/1998/August/6/edluther.asp
http://www.naacp.org/past_future/naacptimeline.shtml