It is far too early to predict what the future of Egypt will be. But the historical parallels with 1979 Iran present some very scary possibilities. Egypt has been a target of exportation of Iranian Islamism for decades and Sudan has been the transit point for much of it. At times, Iran considered Egypt to be the bridge too far, and at others a key to the future Caliphate.
The international political justification for positions on the Egyptian situation are particularly interesting. Many politicians and many protesters were asking the Egyptian Military to take over from an elected leader, in order to establish democracy. The same parties that claim we should not impose Western ideals of democracy on Middle Eastern nations were calling for the overthrow of a democracy by the minorities as a means of democracy. The same parties that so vocally oppose military leaders, even when elected to office, such as Musharraf, were calling for the Military to take over, in Egypt.
Carter had ordered the Shah to allow the Ayatollah to be allowed to return from exile.
In Egypt, the Muslim Brotherhood is unknown in size, as membership is secret, but it is Islamist and has Islamist goals on the government of Egypt, as well as the World Caliphate, including the United States. We simply don't know if the new military leaders are members of the Muslim Brotherhood or not. We do know it espouses violence against rulers like Mubarak, leaders of Tunisia, Jordan, and Bahrain, as well as, Israel. We also know that it has a plan to invade by migration, conversion, and subversion the United States.
In the political spectrum, the Muslim Brotherhood is a minority in Egypt. It has historical ties to Nazi Germany and many of the same platforms. The Nazi (Nationalist Socialist) Party was also a minority party when it took over Germany. It had 25% of the vote, in the 1930's. In the last elections, the MB candidates were shut out by the voters, so it is not the prevailing position of Egyptians.
There is a particular danger in the way things came about in Egypt. When the non-experienced take the reins of government, it takes time to learn how to make things happen. Popular ideas can have detrimental consequences. Who would oppose higher wages, but the implementation can bankrupt governments and private employers alike. This is not to say that Egyptians did not have valid complaints, but that a smooth transition of government requires time. Mubarak was correct in his assertions of handing it over to the next elected President.
The Military of Egypt, spurned to take the reins by the Obama Administration, has several months to learn how to govern, to solidify their power, and to decide if they want to give it up. In this case, a military dictatorship could be the best short term result, but rarely does a military dictatorship maintain respect for Human Rights. Conversely, many nations have relied on the military to step up when the political taskmasters go awry.
Batista was originally a lowly NCO in the Cuban Army when he overthrew an elected tyrant. He was later elected to the Presidency of Cuba and was by all accounts one of the least corrupt Cuba had ever known. While during the entirety of Batista's rule, fewer than 1000 were killed on both sides of armed battles, along with a few civilians. Castro rounded up tens of thosands in his first few days. Thousands were slaughtered.
Batista was not overthrown by Castro, but ordered into exile by David Eisenhower, (Secretary of State under his brother Dwight Eisenhower). Cuba's Treaty with the United States called for US Military Intervention should a dictator ever seize power, but Castro would thumb his nose at the United States for decades to come. Cuba still lives under the oppression caused by US pressure to undermine an ally.
To this day, Liberians believe the United States, under Jimmy Carter, ordered the military coup there, and that the United States, under Bill Clinton, ordered the escape of Charles Taylor, who began the rebellion against the first elected President of Liberia, from the indigenous tribes. Violence begets violence.
Samuel Doe came to power in a coup that killed a dozen politicians, had the Constitution rewritten, and was elected to the Presidency. He died a horrible death under the eyes of peacekeepers, at the hands of a current Senator in Liberia. Charles Taylor escaped from a US jail and spent a couple of years in Libya training his invading rebel army. The next 15 years would pit government forces against rebels in one of the most atrocious of wars, more akin to gang warfare than military conflict, that the world has ever known.
Hugo Chavez attempted mulitple coups in Venezuela, before he was elected to power. The United States (Bush Jr.) opposed a coup against Chavez, after Chavez had established his dictatorship, because he was still considered an elected leader.
The future of Egypt is far from certain. The parliamentary system in place in most of the rest of the world's democracies, including Egypt, allows for minority parties to have great influence, while major parties are shut out of the process. Despite the desires of the average protester, Egypt could become a military dictatorship, an Islamist state, or a shining example of democracy in the Middle East, but it was already one of the most free in the Middle East, and about the closest thing to a moderate government.
Egypt was a place for diplomacy to be used, where rational discussion between US Diplomats could have influenced Mubarak towards greater democracy over the last 2 years. The new rulers of Egypt may not be as friendly to US Interests or as interested in peace with Israel. We won't know the results for weeks, months, or years.
What we do know is that those that fail to understand history are doomed to repeat it. What we do know is that protests against friendly governments are breaking out across the Middle East. What we do know is that those sparked in Tunisia, where it all started, have brought a return of Islamists and a surge of refugees fleeing the violence. What we do know is that many of those countries have much greater support for Islamist Terrorism. What we do know is that the current administration was silent when Persians protested Iran's fraudulent elections. What we do know is that many populist movements have led to majority oppression.