Napolitano appeared on CNN's "State of the Union" along with Michael Chertoff, homeland security secretary during the Bush administration. Both said the pastor should not be prevented from expressing his opinions.
The Rev. Terry Jones, pastor of a tiny congregation in Gainesville, Fla., caused an international uproar by threatening to burn copies of the Muslim holy book. After saying the event was on and off again, Jones finally said he would not burn the Korans.
But violent demonstrations continue overseas, including Afghanistan, and U.S. officials have said Jones put U.S. service members in danger with the mere threat.
"This minister (has) a little small church, in part it's a creation of the media, but it goes across the Internet and across the globe as an accelerant," Napolitano said, "and (demonstrators overseas) don't appreciate that we are a country with freedom of speech, freedom of expression, freedom of religion -- this is just one small minister who we all disagree with on a values basis."
"Part of the problem is the media jumps on top of the story, it does get on the Internet, and, of course, that is very hard to calibrate the context on the Internet," Chertoff said. "And I think the political leaders have to make a judgment about whether they can continue to ignore it in the hopes it goes away or whether they have to address it. "
Asked whether the United States should curb freedom of speech for security reasons, Napolitano said, "No."
Chertoff said: "I don't think we can do that. ... I think what you have to do is you have to fight bad speech with good speech. And that means people who have contrary points of view, and more tolerant points of view have to get out there and talk about it. Part of the responsibility of the media is to cover that, again, in context, and not to give a disproportionate amount of time to people who say extreme things and ignore the people who say more balanced things."
Campus cop fatally shoots Texas student during traffic stop
Exploding whale video goes viral on Internet