In a politically-charged atmosphere, US Secretary of State Hillary Clinton was met with protests from opponents of the Muslim Brotherhood, who claim the United States somehow helped the party narrowly win the elections.

In Alexandria, she was taunted by chants of "Monica, Monica" by tomato-throwing demonstrators who tried to pelt her motorcade with objects including shoes as it left. Clinton's vehicle was not hit.

The chants, referring to the Monica Lewinsky scandal when her husband, Bill Clinton, was president, were heard outside the US consulate as she visited for its reopening.

An embarrassed Egyptian security official said they were chanting "Monica, Monica" and "Irhal, Clinton" (Get out, Clinton.)

Tomatoes, shoes and a water bottle were thrown at part of Clinton's motorcade as it pulled up, protected by riot police, although a US official said Clinton's own vehicle was not hit.

The protest appears to have been the result of suspicions that Washington had helped the Muslim Brotherhood win elections in Egypt in the wake of last year's ouster of president Hosni Mubarak after 18 days of massive street protests.

She sought to dismiss allegations of US interference in the elections.

"I want to be clear that the United States is not in the business, in Egypt, of choosing winners and losers, even if we could, which, of course, we cannot," Clinton told the ceremony at the Alexandria consulate, which had been closed since 1993.

Clinton met Sunday with Egypt's top military leader urging him to support a transition to civilian rule amid fears that the promise of hard-won freedoms could be slipping away.

The top US diplomat also held talks with officials from the 10 million-strong Christian community, and vowed Washington was "committed to protecting and advancing the rights of all Egyptians: men and women, Muslim and Christian."

Clinton's brief trip to Egypt comes as a complex power struggle is being played out between the newly-elected Islamist president, Mohamed Morsi, and the Supreme Council of the Armed Forces (SCAF).

After meeting Morsi on Saturday, Clinton spent more than an hour Sunday in talks with Field Marshal Hussein Tantawi -- the country's interim military ruler after president Hosni Mubarak was ousted last year.

"They discussed the political transition and the SCAF's ongoing dialogue with President Morsi," a State Department official told reporters, adding promised new US aid to Egypt was also on the agenda.

Tantawi later vowed the military will not let "one group" dominate the country, intensifying a standoff with the Muslim Brotherhood from which the new president emerged.

"Egypt will not fall. It is for all Egyptians and not just one group ... The armed forces will not allow it," he said in statements carried by the official MENA news agency, in apparent reference to the Brotherhood.

Clinton has repeatedly called on the military to respect the outcome of the elections, and on Sunday also met separately with Christian and women leaders to hear about the situation for people on the ground.

She said after her talks people "have legitimate concerns and, I will be honest and say, they have legitimate fears about their future."

"Democracy is not just about reflecting the will of the majority. it is also about protecting the rights of the minority," she insisted at a later ceremony to reopen the US consulate in the port city of Alexandria.

"No Egyptian, no person anywhere, should be persecuted for their faith."

She later flew to Israel for talks with Israeli leaders set to focus on the political changes sweeping the Middle East, including in Egypt, the stalemated Middle East peace process and Iran.

Morsi, Egypt's first democratically elected president, is locked in a standoff with the military after he ordered parliament to reconvene, defying an army decision to disband the house.

A declaration issued by the SCAF before Morsi was sworn in -- which acts as a temporary constitution -- granted the military sweeping powers, including legislative control, even though they handed over to Morsi on June 30.

While Morsi's decree was applauded by supporters, it set off a firestorm of criticism from opponents who accused him of overstepping his authority.