The Egyptian military sounds like a rational actor, it does not have the hardline views of some others, is not subservient to any higher power like Gaddafi/Assad... and its highest interest seems to be self-preservation.
Basically this. Anyone member there exact stance during the protest/revolution? Right at the start senior commanders (can't remember exactly who) put out a statement saying something on the lines of "we're not going to get involved in all this business, neither to support nor overthrow Mubarak, it would taint the whole military, whose sole purpose is to defend Egypt. We will stand around in the streets and give the appearance of safety though."
Of course, as a rough estimate of the professionalism and discipline of the Egyptian (cults of personality notwithstanding, I would generally argue that the more disciplined and professional an army is, the less likely it is to slaughter its own civilians) they are the only force in the world to even come close to winning a war against Israel (the 1979 Yom Kippur War). I'm lucky enough (kinda) to personally know three people who were there (two as combatants, one as a journalist
1). The Egyptians came extremely close to driving the Israelis into the sea. Seriously, if you have any interest at all in warfare modern or otherwise, you should really read at least the wikipedia page on it, The Crossing, early pwning of the Israeli armored counterattack by entrenched Egyptian infantry with antitank weapons and the Israeli commando raids/ surprise counterattacks that meant we are still living in a world yet to have a full scale nuclear war, very interesting stuff.
What I'm trying to say is that the Egyptian army is a well trained, modern, disciplined force, as opposed to a bunch of poorly paid unwilling conscripts/highly paid mercenaries with no loyalty, so they're much less likely to massacre their own people.
That said, I have been hearing a lot of rumors from Egyptians I know that the army has been having trouble paying their soldiers at the moment and that they (the army, in the sense of the large body of humans who derive a living for their families from military service, as opposed the official entity that protects Egypt, recruits and trains soldiers and fights wars) are getting pretty pissed off at the MB (as the group nominally in charge who should be making sure shit like that ticks over like clockwork), which if true can't be good for their future power. After all, its one thing to have people to oppose you for ideological reasons but quite another to have them do it because you are so incompetent that everyone can see it.
1. My dad was the journalist, and he was almost killed at the start of the successful part of Israeli counterattack. He was in a trench with the squad he'd been assigned to follow, relatively far back from the front, but still close enough because the Egyptians were basically fortified in a long, fat line along the Israeli side of the canal. He got out to take a piss, moved a bit away and was sprayed with the body parts of the Egyptian soldiers he'd been making friends with for the last week as a mortar shell hit the trench. He had a full on mental breakdown that took him about a year to recover from.
The other two were the grandfather (an Egyptian, radio operator) of one of my best friends from school and the father of my first serious girlfriend (an Israeli, a tank commander (he commanded a tank), took part in the failed initial armored counterattack, came through completely unscathed).