There's a whole host of things people just don't get.
This is not a revolution prompted or backed by Islamic fundamentalists, the Muslim Brotherhood in particular. Not even close. This revolution was prompted largely by the embarrassment of seeing what the people of Tunisia did. The people of Tunisia had had enough, and the people of Egypt realized they'd had enough a long time ago, and the Tunisians prompted the people of Egypt to finally act.
The people of Egypt, all of them, are doing this. Young and old, Muslim and Christian, men and women (some veiled, some not) are all standing side-by-side in this. They want what we want, jobs and security. They've seen the center of the Arab world dwindle down to a seat of poverty, illiteracy and despair. That's what this is all about.
The Muslim Brotherhood, especially since 1970, has been anti-violence. While they do have as one of their stated goals the Qu'ran and Islam as being the only world religion, they do not promote violence as a means to that end. Every time someone within the Muslim Brotherhood promotes violence, they end up breaking away or getting kicked out of the Brotherhood. The Muslim Brotherhood can be thought of as the flip-side of non-violent Evangelical Christians, i.e., really, really annoying but not violent.
In Iran, 90%, maybe 99% of the people support the regime there, and support a religious State. Not so in Egypt. The people of Egypt don't support the regime, nor do they want it replaced by an Islamic State.
The people of Egypt revere the Egyptian Military as bone fide heroes. Not in a fake way like the US reveres its military soldiers as heroes, but in a very real and tangible way. To be a soldier in Egypt is not unlike being a rock star over there. The people love the military, and the military sees its role as protecting the citizens of Egypt against anyone who wold hurt them. They military isn't likely to throw all that way just to keep some crackpot in power, especially a crackpot that the US put in place.
The police, on the other hand, are hated by the people. The police is part of the ministry, directly attributable to Mubarak, and have for years been brutal and totalitarian. The police would slap people around, beat them up, even kill people, just because they could. Notice on the second day of the protests, the police were hard to find. They knew. Right now in Egypt, being a cop is about as popular with the people as being in cop in Juarez is with the drug cartels, and both have the same fate waiting for them. The only difference is, the cops in places like Juarez are trying to do good things, but the cops in Egypt are more like the cartel members.
The US has security and other interests in the Middle East. Yes, the free flow of oil and an open Suez Canal is a part of that, but those are not the primary interests. The primary interest is that of stability in the region. Unfortunately, promoting and installing stability is a double-edged sword, which is why the US is in a very uncomfortable position right now. It is unfortunate that the quickest and easiest way to ensure stability, albeit for a relatively short term, is to install and back a dictatorship who will do things they way we want them to, to keep things stable.
Of course, a dictatorship comes with absolute power, which corrupts absolutely. And the US is once again in the untenable position of having backed a brutal dictator while ignoring the people. What OVM notes above won't take a couple hundred years - it's already here - and the US is scrambling to put its best face forward and show itself as backing the people for a democratic change. It doesn't matter what administration is in office, the US is gonna look bad no matter what. But Hilary certainly isn't making things any better by saying things like, “the legitimate needs and grievances expressed by the Egyptian people," is what Mubarak needs to respond to, while knowing full well those grievances have been legitimate for more than 25 years and the people of Egypt have asked the US many times to intervene throughout the years, and were answered with silence.
There will probably be some small incidents with the people and the military, but probably not widespread. The longer it takes for Mubarak to be removed from power, the more that "mob rule" will begin go take hold. The military isn't likely to try and quash the mobs, either, other than to protect the people (and probably the national treasures like museums). With the rise of mob rule and chaos there will be an increasing Islamic Fundamentalist presence, for sure. Can't let that opportunity go by.
But as things get more out of control, the greater is the chance for a straight military take-over of the government. And it will be done to protect the people. Before too long there will be thousands of foot soldiers in the cities, but they will not fire on the people, I believe. If they fire on anything, it will be on Mubarak's residence, at the loyal ministry police who are charged with protecting Mubarak. The people want Mubarak out, and were quite insulted that he appointed what is seen as just another US puppet as his Vice President.