There have been a lot of great observations by you all on the effects of religion on this, and other situations, which I dare not add to even if I could.
What I can add though is never forget about the importance of "brotherhood" in both secular and deeply religious societies. That typical 'mans' habit of grouping or bonding together in a common shared sense of belonging. It has driven conflict for centuries, and I see no evidence of it changing any time soon.
When this happens blood brotherhood seems to overtake religion. Exceptions are of course scattered throughout history, with say the Christian Crusades and Elizabethan stand against Philip of Spain, in particular during the 1580s, culminating in the Spanish Armada of 1588, coming to mind.
But when Britain declared war on Germany in the August of 1914 their was open jubilation on the streets, with a chance to fight the growing threat to the Empire of the Hun. No talk of religion as both were Chritian countries, and all rememberance of the Prussian army saving Wellington's bacon at Waterloo was forgotten. I fear to say that even now many men would come together over any talk of fighting the French again (heaven forbid!!). On that point even the welling patrisism, nationalism, and desire for world power for a new Empire took the Royal Navy fleet into battle against the French and Spanish fleet at Trafalgar on the 21st October 1805. Once again no talk of religion. Chartism caused great groups of multi-religious and secular groups to come together during 1838-48, for the "Common Good".
The Nazis invasion of Russia on that infamous day of 22nd June 1941 was all about world domination and ridding Germany of the communist threat yes, but probably more about the hatred felt by the 3.6 million Germans involved towards the Russians.
What am I really saying? Well I believe, and it is purely my viewpoint, is that mans natural desire to group for battle, for a cause, is far stronger than the one of grouping over religion or politics. Men in these groups think of honour first, the upholding of the cause, fighting the battle together, then perhaps later justify it with politics and religion.
The Middle East situation is very complex, but as usual what comes first in any talk of battle is fighting the Jew, or Palestinian, or Western power, then actually about the religion that may be behind those groups. The lack of trust, as existed between Great Britain and Germany before the Great War, is really the spark that ignites conflict, with religion secondary.
In Egypt this will result in first the fight, now well advanced, to remove the regieme untrusted by most Egyptians. The dust will then settle, and as in Iran after the Shah was deposed, the momentum to fill the vacuum is taken up by the secular or religious factions, whoever they will be. They may well cause a secondary battle for political power, where the religious element becomes important. But that does not mean that really the aims of any group is one of gaining power, nothing to do with religion, which in fact has been a smokescreen, an excuse, as in fact it always was in all past historical conflicts.
That grouping of men in the common cause who have caused battle to ensue, and lives to be lost, need an excuse to justify their actions. "In the name of God or Allah" becomes then the common cry!
History rolls on, and mans inhumanity to man continues, often finally in the name of religion, which is actually the biggest crime of all! So as we watch Egypt, and the other nations in those parts playing their power games, remember it really is about mans power over other men, not about the God most of us worship!