The attack may have been triggered by complaints about noise coming from the church during Friday and Saturday services by a Muslim family living next door, local authorities said. The Muslims called the church an "unlawful neighbor to the Muslims who live adjacent to it and must therefore be moved."
The church itself was not the intended target of the arson, a local police official told Egypt's independent Al-Hayat TV channel. Rather, he said, the attack aimed for a room adjacent to a community center that the Copts wanted to build without a license.
Demonstrators demanded the church's rebuilding and the prosecution of those responsible for this and prior attacks. Numerous Coptic churches throughout Egypt have been burned by radical Muslims since Mubarak fell two years ago.
The Copts have also been forced into "reconciliation" meetings by government officials that they say are humiliating and result in their losing all of their rights.
The church was attacked during a meeting Saturday in the wake of the arson, the Assyrian International News Agency (AINA) reported. The crowd shouted "We do not want the church" as rocks and Molotov cocktails were thrown at it.
Though the church was attacked and its dome damaged, the reconciliation meeting ended with restrictions imposed on its reconstruction. It cannot be returned to its original height, for example, and the church will have to add soundproofing to the wall facing the neighbor who complained. It was not clear if there would be any compensation for the fire damage.
Sunday's protest included a demand that these reconciliation proceedings cease.