From John Hammer's front-pager (unposted) in today's Rhino:

The Police Chief David Wray resignation story isn't about a black book, although there is a black book in it. It isn't about Greensboro Police Lt. James Hinson or drug dealers, although they are in it. And most importantly it isn't just about race although there are some racial factors that cannot be ignored.

This story is about honesty and trust, and it can be summed up simply: City Manager Mitch Johnson, Mayor Keith Holliday, and [the rest of the Council members] didn't trust former Police Chief David Wray and don't believe Wray was honest with them...

...If everything was on the up and up then why did two of Wray's top officers resign when faced with questions about their activities? If the black book was simply put in the trunk of Bradley's car for safe keeping, why was its existence kept a secret?

According to Occam's Razon, the simplest answer is usually the correct one. In this case the simplest answer is that Wray was, for whatever reason, not honest in his dealings with his boss, City Manager Mitchell Johnson. Any other explanation involves huge coincidences and for people to do things that don't make any sense.