One of the striking 
features of last month's overthrow of Egyptian President Mohammed Morsi 
was the rage that came out in the street demonstrations against the 
Obama administration for its alleged backing of the Muslim Brotherhood. 
A CNN report on June 30
 showed the crowds in Tahrir Square carrying anti-American signs saying:
 "Obama, stop supporting the Muslim Brotherhood fascist regime." Some 
signs were aimed not only against President Barack Obama, but also 
against U.S. Ambassador to Egypt Anne Patterson. 
Where did the crowd get
 this idea? Patterson detected before Morsi fell from power on July 7 
that a significant number of Egyptians believed that the U.S. was 
working with the Muslim Brotherhood. She actually gave a speech on June 
18 at the Ibn Khaldun Center "to set the record straight" on this 
subject. She suggested that some might be asking if the contacts between
 the U.S. Embassy and the Muslim Brotherhood over the years was being 
interpreted was "evidence of a long-term conspiracy to support the 
Muslim Brotherhood to replace the government of former President Hosni 
Mubarak." She explained to her audience that all countries "maintain 
contacts with those out of power." Her logic was simple: "Today's 
political outcasts may be tomorrow's leaders."
However, at the end of 
her speech she appeared to be taking a position against the planned 
anti-Morsi demonstration: "Some say that street action will produce 
better results than elections. To be honest, my government and I are 
deeply skeptical." For Egyptian critics of the Muslim Brotherhood, 
Patterson's words amounted to direct intervention into Egyptian domestic
 politics. The respected Lebanese daily An-Nahar added that Egyptian 
liberals felt that the U.S. had failed to criticize Morsi's 
authoritarian practices since he came to power, leading them to conclude
 that "Washington was 'in bed' with the Brotherhood." 
What enraged these 
Egyptians even further was Patterson's visit the same week of her speech
 with Khairat el-Shater, the deputy head of the Egyptian Muslim 
Brotherhood, who is widely regarded as the strongest figure in the 
organization. Secular Egyptians can understand when the U.S. ambassador 
meets with Egyptian officials who also happen to be members of the 
Muslim Brotherhood. But if she met with the leadership of the 
organization, outside of the framework of the Egyptian government, then 
that is interpreted by Morsi's opponents as an effort to legitimize the 
Muslim Brotherhood, even if it was not the intent of the U.S. 
ambassador.
In order to halt the 
spread of the rumors about the links between Washington and the Muslim 
Brotherhood, Secretary of State John Kerry was forced to add his voice, 
last week: "We firmly reject the unfounded and false claims by some in 
Egypt that the United States supports the Egyptian Muslim Brotherhood or
 any specific Egyptian political party or movement." 
Yet this claim had 
become the conventional wisdom across the Middle East. The Wall Street 
Journal reported that when then-Secretary of State Hillary Clinton 
visited Cairo just before Morsi issued a declaration giving himself 
powers over the judiciary, there were suspicions that he had U.S. 
support, since Washington did not condemn him for what he had done.
Many in the Middle East
 have been surprised at U.S. policy toward the Muslim Brotherhood. 
Having provided political asylum for Muslim Brotherhood members fleeing 
Nasserist Egypt, after 9/11, Saudi Arabia completely revised its policy.
 Its late crown prince, Nayef bin Abdulaziz, called the Muslim 
Brotherhood "the source of all problems in the Islamic world." 
A former Kuwaiti 
minister of education wrote in Asharq Al-Awsat in 2005 that "all those 
who worked with bin Laden and al-Qaida went out under the mantle of the 
Muslim Brotherhood." The main architect of the 9/11 attacks, Khalid 
Shaikh Muhammad, came out of the Kuwaiti Muslim Brotherhood, while the 
roots of al-Qaida's current leader, Ayman al-Zawahiri, can be traced to 
the Egyptian Muslim Brotherhood.
In recent years, 
America's Arab allies have expressed their serious reservations about 
the Muslim Brotherhood. In December 2012, the United Arab Emirates 
arrested a number of Muslim Brothers from Egypt who were accused of 
trying to plot the overthrow of the ruling family. In an April 2013 
interview with Jeffrey Goldberg, published in the Atlantic, Jordan's 
King Abdullah described the Muslim Brotherhood as "wolves in sheep's 
clothing." He described Jordan's "major fight" -- to prevent the Muslim 
Brotherhood from conniving its way into power across the region. King 
Abdullah claimed his Western allies were naive about the Muslim 
Brotherhood's intentions.
But it would be 
incorrect to argue that the U.S. connection with the Muslim Brotherhood 
came out of the Obama administration, alone. The problem is deeper. 
Already in 2007, Foreign Affairs, a quarterly which might be seen as a 
weather vane of the U.S. foreign policy establishment, decided to 
publish a controversial article titled "The Moderate Muslim 
Brotherhood." The article was largely based on the conversations of its 
authors with senior members of the Muslim Brotherhood in Cairo. They 
wrote that the Muslim Brotherhood was discouraging jihad. 
Yet on the website of 
the Muslim Brotherhood, the very opposite was written. The Muslim 
Brotherhood explained there in 2003 that it sought to recover "the lands
 robbed from Islam." This was consistent with the writings of Hassan 
al-Banna, the founder of the Muslim Brotherhood, whose newspaper wrote 
that Muslims should take back Spain, southern Italy and the Balkans. The
 web article concluded: "The problems of conquering the world will only 
end when the flag of Islam waves and jihad has been proclaimed." In 
2005, the supreme guide of the Muslim Brotherhood boasted that his 
organization was active in 70 countries. 
The main motivation of 
those in the West who support working with the Muslim Brotherhood is 
that it can serve as an alternative for young Egyptians to al-Qaida and 
other jihadist groups. But that is not what happened in the past. When 
the Muslim Brotherhood came to power in Sudan, it hosted jihadist 
leaders from Osama bin Laden to the heads of Hamas. It even allowed them
 to set up training camps during the 1990s. 
Morsi's regime did not 
go that far, but it pardoned jihadist leaders who were in Egyptian 
prisons, like Mustafa Hamza, the leader of al-Gamaa al-Islamiyya (the 
Islamic Group) who was involved in the attempted assassination of 
President Mubarak and the 1997 Luxor massacre that left 62 dead. Morsi 
also promised to work for the release of Sheikh Omar Abdel-Rahman, the 
mastermind of the first World Trade Center attack in 1993. More 
recently, in March, Morsi was pressing the Egyptian military academy to 
accept members of the Muslim Brotherhood as well as other hard-line 
jihadists. The Muslim Brotherhood was working closely with Hamas. An 
Egyptian general admitted on March 11 to Dubai's Al-Bayan newspaper that
 the Muslim Brotherhood was pressuring Defense Minister Abdel-Fattah 
el-Sissi to ignore the tunnels from Sinai to the Gaza Strip.
The perception in the Middle East
 that the U.S. had been sympathetic to the Muslim Brotherhood may be 
overstated, but it is not entirely without foundation. A school of 
thought in Washington exists that truly believes that the Muslim 
Brotherhood has evolved into a moderate organization, with which the 
West can do business. It has been influencing policymaking since the 
second term of the Bush administration. But it is too early to establish
 whether the overthrow of Morsi will lead to the demise of this 
dangerously naive political theory or whether it will resurface in one 
of the other Arab states facing internal revolts as part of the Arab 
Spring.