The Associated Press reports: The head of Egypt’s military took a tough line Sunday on the Muslim Brotherhood, warning that he won’t let the fundamentalist group dominate the country, only hours after U.S. Secretary of State Hillary Rodham Clinton urged him to work with Egypt’s elected Islamist leaders.

Clinton’s visit to Egypt underscored the difficulty Washington faces in trying to wield its influence amid the country’s stormy post-Hosni Mubarak power struggles.

Islamist Mohammed Morsi, a longtime Brotherhood figure, was sworn two weeks ago as Egypt’s first democratically elected president. Led by Field Marshal Hussein Tantawi, the military handed over power to him June 30 after ruling Egypt for 16 months. The military, however, dissolved the Brotherhood-led parliament and stripped Morsi of significant authorities in the days before his inauguration, while retaining overwhelming powers for itself, including legislative power and control of the writing of a new constitution.

The United States is in a difficult spot when it comes to dealing with post-Mubarak Egypt — eager to be seen as a champion of democracy and human rights after three decades of close ties with the ousted leader despite his abysmal record in advancing either.

This has involved some uncomfortable changes, including occasional criticism of America’s longtime faithful partners in Egypt’s military as it grabs more power and words of support for Islamist parties far more skeptical of U.S. intentions in Egypt and the rest of the Middle East.

That has fueled accusations among some Egyptians who back the military or oppose Islamists that Washington is promoting the rise of the Brotherhood to power. Protesters chanting against the U.S. — sometimes reaching several hundred — have sprung up at several sites where Clinton visited this weekend. On Sunday, protesters threw tomatoes, water bottles and shoes at her motorcade as she left a ceremony marking the opening of a new U.S. consulate in the Mediterranean city of Alexandria.