Robert Parry has a very good article explaining why he thinks the media self-censors.
It has a lot of important history, showing how the pressure to "fix the intelligence," whether at the CIA or at the New York Times, goes back to the Cold War.
Through bureaucratic bullying and purges, the neoconservatives eventually silenced CIA analysts who were reporting evidence of Soviet decline. Instead, a "politicized" CIA analytical division adopted worst-case scenarios about Soviet capabilities and intentions, estimates that supported the Reagan administration's costly arms buildup and covert wars in the Third World.
The second important target in these Neocon Wars was the U.S. national press corps. The strategy here was twofold: to build an ideologically conservative news media and to put consistent pressure on mainstream journalists who generated information that undercut the conservative message.
The so-called "controversializing" of troublesome mainstream journalists was aided and abetted by the fact that many senior news executives and publishers were either openly or quietly sympathetic to the neocons' hard-line foreign policy agenda.
As the years wore on, the survivors of this bureaucratic Darwinism -- who had avoided the Right's wrath both in the worlds of journalism and intelligence analysis -- rose to senior positions in their respective fields. The ethos shifted from truth-telling to career-protection.
This rings true to me whereas other common explanations, such as advertiser pressure, do not.