The report is based on a questionnaire sent to partner organizations of Reporters Without Borders (14 freedom of expression groups in five continents) and its 130 correspondents around the world, as well as to journalists, researchers, jurists and human rights activists.
Just to be clear they are professionals with an interest in freedom of speech, not some random group of people with an axe to grind.
I imagine the main problems in the US have to do with national security issues, I recall several high profile cases where journalists were forced to reveal sources, and a general fear of lawsuits among the big publishing houses, although this is hardly unique to the US. Controversial investigative journalism has had a hard time this last decade as news outlets are pretty much only about making money and not so much any more about fulfilling their part in the system of checks and balances.