Revolutions often encounter problems when the force that united people against an enemy fails to provide a common vision for the future. In Egypt's case the internal divides, like any society's, are complex - with fault lines between class and in rural and urban areas. The most reported division, although not the deepest, is along sectarian lines between Sunni Muslims and Coptic Christians.
It's a divide that the former regime is accused of exploiting. The former interior minister, Habib el Adly, is being investigated in connection with the New Year's Eve bombing of a church in Alexandria, which was allegedly carried out to rally support for the regime.
Members of the former regime are facing a barrage of charges, but this one rings true for most Egyptians, particularly after the 18-day uprising earlier this year. Those 18 days were some of the most lawless in Egypt's recent history, but not a church was touched nor were widespread attacks against Christians reported.
Where was this widely felt sentiment of sectarianism? (Incidentally, the synagogue next to Tahrir Square was also left untouched.) On the contrary, Tahrir demonstrations saw Muslims and Christians united in protest and prayer.
Many have been shocked by the violence this month when two churches were burnt in the Imbaba district of Cairo and at least 12 Muslims and Christians were killed. Blame immediately fell on elements of the Salafi movement, and 23 have since been charged with terrorism and murder.
The Salafis are known for being, for the most part, an ultra-conservative, inward-looking group. In recent months, many Egyptians have come to fear that Salafis want to put their imprint on society at large - which explains public opinion's quick judgement against them in the Imbaba case.
But the story leaves unanswered questions. Some eyewitnesses said that the provocateurs at Imbaba were not all Salafis, who are easily identifiable by the way they dress. There have been other reports that members of the former secret security forces were there.
And so the conspiracy theories begin. Was this a genuine outbreak of Christian-Muslim sectarian violence? Or were there counter-revolutionary forces at work? Other foreign forces?
Many do not want to believe that there is a genuine sectarian problem. But there is, and it does not come only from Muslims. Sometimes it is simply rhetoric - last October, Bishop Abna Bishoy, the secretary of the Coptic Church's Holy Synod, said Muslims were only "guests" in Egypt. More recently, in the aftermath of church bombings, some Copts held a rally outside the US Embassy calling for international intervention.
Of course, the overwhelming majority of Copts oppose these sentiments, just as a similar proportion of Muslims oppose the arson at Imbaba.
This week marked an anniversary in the widest Arab cause - the Nakba and the establishment of the state of Israel. As every year in probably every Muslim and Arab country around the world, there were protests in Egypt to express support for the return of Palestinians to their homeland, the liberation of Jerusalem and the establishment of a Palestinian state.
This year was different in Cairo, however, because the protest was held in a free Tahrir Square. And the sectarian strife of recent months was not forgotten for a moment.
A Coptic mass in the square was followed by the Friday congregational prayer and sermon for Muslims. The imam spoke about the importance of Egyptian unity, quoting from both the Bible and the Quran, deploring that while Muslims and Christians had come together for Egypt's revolution and the Palestinian cause, they could be divided by sectarian issues.
There were two simultaneous rallies going on, one that insisted that Egyptian unity was paramount, and one that supported the Palestinians. The two causes were practically seamless.
At the television station not far from Tahrir Square, another rally inspired by the Imbaba arsons included Christians and Muslims standing together - although there were different opinions on who was responsible and acted first in the violence, with blame falling on both Salafis and former regime loyalists.
Simply that these joint statements are needed shows that, despite the efforts of some Egyptians to deny the sectarian divide, it does indeed exist. It is not the main fault line, when considered next to economic, class and the urban-rural divisions, but it does create problems. It is an easy target for manipulation, as reflected by charges against members of the former regime.
Yet it is also clear that Egyptian unity is far stronger. The sense of patriotism is more mainstream than the sense of sectarianism. In Tahrir Square, we were reminded time and time again of the best of what it meant to be an Egyptian. Now Egyptians must find the best within themselves, and together, they must confront the worst.
Dr HA Hellyer is a fellow of the University of Warwick and of the Institute for Social Policy and Understanding