The world has seen many military coups in the course of history. In places like the Byzantine Empire it became the established means of changing rulers. Since the age of the enlightenment it has not been considered to be a legitimate form of democratic process.
Gen. Nassar staged a military coup in 1952 that overthrew the Egyptian monarchy and brought the military to power. They have remained in power ever since. When Anwar Sadat began to chart a political course that they didn't approve of he was assassinated. Mubarak was put in his place.
In 2011 there was growing political unrest in Egypt. The military seemed to choose to step aside and allow Mubarak to be deposed by the popular will. People in the west took that to signify an end to military rule. Things really didn't work out that way. There was a process of drawing up a constitution and holding elections. However, the government of Mohamad Morsi has not been effective at establishing a working political consensus and the mobs returned to the street.
Now the military has decided to call it off and start over. They have deposed Morsi and have jailed key figures from the government. Now the supporters of that government are out in the streets and some of them are being shot by the military.
A great many people in the west are viewing this action by the military as necessary because they didn't like the policies of Morsi and his supporters in the Muslim Brotherhood. I certainly wouldn't argue that they seemed to be headed in a positive direction. However, it seems to me that you either have a constitutional democracy or you don't. Simply because you don't like get the people that got elected, doesn't invalidate the constitution.
What seems to me to be an accurate way to view the situation in Egypt is that there has been no real break in the long period of military rule. The military has learned some things about western marketing technique. As an "interim" caretaker, they put a faceless technocrat in charge, instead of a general dripping gold braid. It looks better on TV.
Even if they do follow their announced plan for drawing up a new constitution and holding new elections, it seems plausible that the resulting government will serve at the pleasure of the military.
I am quite aware that there is no way that the US government is going to refrain from trying to influence political affairs in the Middle East. It is a major confluence of geopolitical and economic forces. However, it seems deluded for Americans to expect political events in societies with histories and cultures that are fundamentally different from our own to look like they were made in the USA.