For my money there is no better Egyptian analyst of the religious scene than Hossam Tammam — he's a specialist on Islamists, but what he writes here goes for the Coptic Church too.
Any discussion of the status of Islamists in a new Egypt makes little sense if it’s based on the same data that was previously used to study religious movements, and if it ignores the fact that Egypt has witnessed a revolution that destroyed many of the old features of its religious scene.
The revolution was not just directed against the autocratic, repressive and corrupt Egyptian regime, which relied on an alliance of money, power and corruption. It was also directed against the official religious establishment and its discourse that supports this regime, either directly or indirectly.
The Egyptian revolution has completely reconfigured the religious scene and clarified the public’s position towards religious institutions and discourses in the country. The result has been surprising. No one expected that religious Egyptians are capable of overriding the powers of religious institutions and of challenging religious discourses that they suddenly perceived as part of a corrupt and repressive regime.
The official religious establishments--both Islamic and Christian--have been the biggest losers in the revolution.
Personally, I hope this episode gets people to consider their religious leadership and moves them to move to either change church (or for Muslims ignore al-Azhar) and ignoring religious issues when addressing politics.