Following the ouster of Mubarak in 2011, sectarian violence rose, and attacks on churches sent thousands of Coptic protesters into the streets.
A protest in October 2011 was violently quelled by the country's military rulers, leaving 26 people dead and sparking further outrage.
The violence has abated, and 2012 was characterized more by the struggle for political and religious rights, said Hossam Bahgat, the director of the Egyptian Initiative for Personal Rights.
“It is not actual frequent sectarian violence, it is fear of further marginalization and second class citizenship,” he said, adding that Egypt has been deeply polarized as it drafted the constitution.
Ishak Ibrahim, a researcher who monitors religious freedom cases in Egypt, said Coptic Christians are facing two new sets of problems: cases of insulting Islam and fear for their life style because of increasingly assertive radical Islamists.
In October, two Coptic boys were put in a juvenile detention after locals accused them of urinating on pages of the Quran, Islam's holy book. It was one in a series of cases against Coptic Christians in the same period, following the fury over an anti-Islam film produced in the United States. The case against the boys was later dropped after mediation.
Ibrahim said some wealthy Copts, who have connections abroad, have temporarily sought to leave Egypt.
“But the majority (of Christians) are also less fortunate,” he said. “Like most Egyptians, they are with little education and have difficult economic conditions.”