The 27-year-old actress, who stars in a new film called "The Great New Wonderful" (search) about the 2001 terror attacks on the World Trade Center, said in an interview last week that the United States "is responsible in some way" for the attacks.
A fan Web site devoted to Gyllenhaal was overwhelmed with criticism, forcing the site's editor to remove the ability to post messages "because it's gotten too outta hand."
In a statement issued Monday by her publicist, Gyllenhaal said Sept. 11 was "an occasion to be brave enough to ask some serious questions about America's role in the world. Because it is always useful as individuals or nations to ask how we may have knowingly or unknowingly contributed to this conflict.
"Not to have the courage to ask these questions of ourselves is to betray the victims of 9/11."
She also expressed her grief for "everyone who suffered and everyone who died in the catastrophe."
"The Great New Wonderful" features stories about people living in New York in the aftermath of the terror attacks. The movie is being shown at the Tribeca Film Festival (search), which was founded by Robert De Niro (search) to help revitalize downtown Manhattan after Sept. 11.