Looks like an incumbency effect to me. Bush was in office during the campaign and had a higher profile and therefore had more targets to aim at, especially given the high profile divisiveness of the Iraq war (you could criticise Kerry's views on the war, but not his handling of it).
This seems to be supported by the fact that when the same people ran a similar survey for the 2000 campaign, they found a decided tilt towards Bush:
The Last Lap
For example:
"In the culminating weeks of the 2000 presidential race, the press coverage was strikingly negative, and Vice President Al Gore has gotten the worst of it, according to a new study released today by the Committee of Concerned Journalists... George W. Bush was twice as likely as Gore to get coverage that was positive in tone. "