One of the big stories in Mexico this week (not to mention one of the biggest Mexico stories in the US) revolves around the murder of an El Diario intern in Juárez, and the subsequent front-page plea by the paper for a truce with the drug gangs. This attempt to carve out some sense of what would be acceptable for the gangs led to a condemnation from the federal government, on the grounds that no one should try to negotiate with organized crime.
There's no question that when societal institutions outside of the government start to show a willingness to find an MO with criminals, it undermines attempts by the government to unite all of the nation in steadfast opposition to organized crime. It makes it easier for other groups to negotiate wth crime as well. Nonetheless, it's really hard to blame newspapers for wanting to live in peace. The government's frustration is understandable and valid, but the newspaperman's desire to see his children grow is far more so. Furthermore, Calderón's team is in a sense reaping what it has sown. It has spent precious little effort to protect reporters, neither as regular citizens whose job makes them a target, nor as a special industry necessary to the operation of a free society. Even if Calderón's team had done a lot more, newspapers would still likely be in the crosshairs, but given that they've done next to nothing, it's logical that newspapers would decide that their safest bet lies in seeking accommodations with criminal groups.