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People shout and hold slogans in front of the U.S. embassy during a protest in Cairo on Sept. 11.MOHAMED ABD EL GHANY/Reuters

In the wake of the deadly attacks on Americans in Libya and disappointment in Washington with Egypt, experts say it's just the tip of the iceberg of unrest across the Muslim world.

Anti-American protests have spread since Tuesday night when mobs swarmed the U.S. embassy in Cairo and the U.S. consulate in Benghazi, Libya, and they show no signs of abating. Protesters say they object to a U.S.-made film that denigrates the Islamic Prophet Mohammed but, behind the lines, a much larger motive has propelled the organizers to take action.

"Make no mistake," said Barry Rubin, director of the Global Research in International Affairs Center in Israel, "this is a war, not a misunderstanding. It is a battle of ideologies and a struggle for control of state power, not hurt feelings over some obscure video."

Sunni Islamic extremists in both Libya and Egypt are looking to take control, using the post-revolutionary chaos in both countries to their advantage.

In Libya, as the International Crisis Group notes in a report to be released Friday, "armed Islamist militias influenced by al-Qaeda are growing ever stronger in and around eastern Libya, raising fears about the country's stability and the likelihood of further deadly attacks like the one that just killed the U.S. ambassador."

These Islamists, broadly known as Salafi jihadists, did not contest seats in parliamentary elections in July, believing, as they do, that there is only one law, that of God as recorded by Mohammed, and no need for any parliament passing other laws.

They are using other means, now, to press their case.

"They see Americans as patrons of a regime they don't like," the American-born Mr. Rubin said. "They don't want to thank us for helping liberate them; they want to run us out of the region entirely."

As bad as that may be for U.S. interests in Libya, much more is on the line in Egypt, another post-revolutionary state where Salafists are taking a similar anti-American tack and the country's Muslim Brotherhood President, Mohamed Morsi, is walking a fine line.

The Salafists are trying to embarrass the Brotherhood, Mr. Rubin says. They are trying to out them as supporters of the "anti-Muslim" United States.

Indeed, the ruling Brotherhood doesn't want to lose U.S. support – financial and military – but they don't want to be embarrassed by their Salafist competition.

Mr. Morsi, who appeared in public on Thursday in Brussels to answer questions about the storming of the U.S. embassy Tuesday, reserved his strongest language to attack the contentious film rather than to apologize for, or to condemn, the assault on the embassy.

"In Egypt and everywhere in the Arab world there is anger," Mr. Morsi said, adding that he had pressed U.S. President Barack Obama on the scurrilous nature of the film during a phone conversation Wednesday.

"[But,] it is our duty to protect our guests and visitors from abroad," he added.

"The freedom to express opinions and demonstrate … are guaranteed, but without attacks on private or public property, diplomatic missions or embassies," he said.

The U.S. administration is still waiting to see which way the political wind is blowing in Egypt: Just how far will the Muslim Brotherhood leadership go to satisfy U.S. interests? In the meantime, in an interview Thursday, Mr. Obama underlined the growing testiness between Washington and Cairo when he tried to describe the new Egyptian regime: "I don't think that we would consider them an ally, but we don't consider them an enemy," was how he put it.

For her part, Secretary of State Hillary Clinton went out of her way to denounce the film that appears to have sparked the protests, describing it as "disgusting and reprehensible."

However, in a comment that appeared to be directed at Mr. Morsi, she added: "We all, whether we are leaders in government, leaders in civil society or religious leaders, must draw the line at violence. … Any responsible leader should be standing up now and drawing that line."

The protests that now threaten to spread across the Muslim world are the tip of an iceberg, says Alastair Crooke, a former MI6 analyst and specialist in the Islamic world. He argues that even the recent increase in attacks in Iraq, along with those in Syria being directed against the Assad regime, are the work of the same kind of Sunni extremists, seeking to take power in those two countries.

"It's a region-wide phenomenon," Mr. Crooke said.

"There is a battle going on in the Middle East that will continue for decades," Mr. Rubin says.