The media and the government should be kept separate in all forms. Monitoring the AP by the Justice Department is an overreach of authority by the government, and the effects that this could have on the media (especially in relation to freedom and protection of sources) are dire enough to outweigh the good.
The government will do some sort of monitoring of the press. It is bound to happen. However, the Justice Department needs to have a little more care in how the monitor the Associated Press and other press agencies. There is keeping up with the news like everybody else, and then there is over the top behavior. Unfortunately, that's been all too common recently.