If people were protesting the story, then they're just looking for something to cry wolf about. The story was fine and actually very introspective:
http://www.phillymag.com/articles/white-philly/
As for the magazine not having many Black writers or editors, they could probably say the same thing about many facets of city business, yet they don't because those city businesses don't try to engage in a dialogue. Instead everyone does the go-along to get-along dance that really doesn't change anything. And the flip side is often city government, at least it is in DC, where the proportion of Black city workers far outstripes the actual racial context of the city, but no one says anything.
I read the article and enjoyed it. I particularly liked Jen at the ending because I think her experience is right. My experience in DC was it was more of a class thing, but there was a racial tinge. And of course there were some rough edges. But once I got to know folks, race evaporated. Unfortunately most in the city still choose to self-segregrate and think all sorts of crazy crap about the other race (for instance, that somehow there is tactit acceptance of crimes within the Black community or that whites are on a crusade to gentrify DC with bike lanes--both are ridiculous assertions yet belived by so many folks I know Black and White).