"Run the media" in this context doesn't mean there's some CIA commissar approving every article or broadcast. What it means generally is that access to "leaks", scoops, "anonymous government sources", "high level intelligence officials", etc is predicated on uncritically toeing the "intelligence community" line. Failing to do so means no more access, and you will be replaced by someone else.
Take the lessons of Manufacturing Consent and apply them to the contemporary political context instead of Vietnam and East Timor, even if the elite media seems to be aligned with your own political beliefs.
