Unfortunately, the mob of 40,000 (!) was led by the Islamists of Jama’a al-Islamiya and the Muslim Brotherhood. JAI is the organization that Al Qaeda’s #2 Ayman al-Zawahiri came out of. They’re the guys who assassinated Sadat. Mubarak cracked down hard on them afterwards, thousands were imprisoned, and up to 1,000 were murdered. Typical scenario was to tie you to a post in the desert with no food or water until you talk. Very effective. You don’t talk and you’re dead real quick.
This is also the group that bombed the WTC in New York the first time around. They are led by the so-called Blind Sheik, now in prison. I thought that the mass crackdown wiped them out, but I guess not. Apparently they are back on the streets in huge numbers after the emptying of the prisons by the revolution.
After Mubarak cracked down on them, Zawahiri fled the country with may of his men. He met up with bin Laden in Sudan and ended up radicalizing bin Laden, who was fairly quietist at that point. It was Zawahiri who convinced bin Laden to attack the “far enemy” (the US) instead of the “near enemy” (the pro-US governments in the Middle East.
The embassy attack was pretty hairy. The 8-man Israeli staff hid in a metal room and demonstrators started beating on the walls of the room. A task force of Egyptian intelligence agents dressed up as rioters and mingled with the crowd. They got to the room but could not get in because they did not know the code. They called the head of Israeli Shin Bet to the get the code. They got in and changed the Israelis into Egyptian clothes, then sneaked them out through the mob and put them in armored vehicles to the airport where they were evacuated.
Five security forces were killed and many more were wounded. Security forces pretty much sat back and did not get involved until the crowd attacked a nearby police station, sacked it, and stole its weapons.
In addition, the mob also tried to swarm the Saudi embassy in Cairo, but police and army forces kept them away. This is not being reported by US media sources.
The rightwingers and Israelis were right. This is what was going to happen if you get rid of Mubarak.