As a White House insider, Zelikow's appointment to this task was controversial on grounds of conflict of interest. 
Before the investigation even got underway, Zelikow alarmed Commission staff by writing a detailed outline for the report, "complete with chapter headings, subheadings, and sub-subheadings."
After the staff learned of this outline, some of them wrote a parody entitled "The Warren Commission Report - Preemptive Outline," with one chapter headed, "Single Bullet: We Haven't Seen the Evidence Yet. But Really. We're Sure."
As this parodied outline indicated, Zelikow had decided in advance what the 9/11 Commission's report would say and, as documented by then-New York Times reporter Philip Shenon, used iron-fisted control over virtually every aspect of the Final Report (2004)
Last week Zelikow was again in the news about an earlier 9/11 report, which he did not supervise -- the Joint Inquiry into Intelligence Community Activities (2002). 
This report contains 28 pages, blank to the public, that deal with the financing of the attacks. They were classified 12 years ago by President George W. Bush for national security reasons.
Closely guarded in a basement room under Capitol Hill, these pages may only be read by legislators following a formal application process -- and even then only under the watchful eyes of staffers who forbid note-taking.
A group of 23 members of Congress agree that they shed essential light on the 9/11 attacks and are pressing for their declassification so that the American people might finally have the truth.
On Wednesday, January 7, Congressmen Walter Jones (R) and Stephen Lynch (D), co-sponsors of House Resolution 428 calling for the President to release the information, held a press conference on Capitol Hill, together with three people who had lost family members in the attacks. 
Before and after this press conference, Jones and Lynch were interviewed by national networks, including CNN, CBS, ABC, CBC, and Fox News.
In at least two cases, news agencies referred to statements by Zelikow, who, after running the 9/11 Commission returned to academics at the University of Virginia in 2007, where he is now:
The CBS anchor commented: "Philip Zelikow, who was the executive director of the 9/11 Commission, says that the pages should not be released, saying that the pages are full of unproven facts." (Congressman Lynch replied that the same people who wrote these pages drafted the entire report, the rest of whose 858 pages have been public all along.)
Newsweek reported: "Philip D. Zelikow, who was executive director of the 9/11 Commission, and has read the pages, thinks they should remains secret. Now a professor of history at the University of Virginia, Zelikow compared the 28 pages to grand jury testimony and raw police interviews -- full of unproven facts, rumors and innuendo."
Equally intriguing is that Zelikow fired a 9/11 Commission investigator, Dana Leseman, back in 2003 over the same issue. Leseman and a colleague had been researching a possible link between two of the 9/11 hijackers -- Khalid Almihdhar and Nawaf Alhazmi -- and elements of the government of Saudi Arabia.
Leseman asked Zelikow to provide her with a document she needed for her work -- 28 redacted pages from the 9/11 Congressional Inquiry report that she herself had helped to research -- but Zelikow blocked her access to it. This led to an argument that resulted in her dismissal. 
The situation now is that just as President Bush had the authority to censor the pages, President Obama has the authority to release them.