The ruling concerning the churches that are in Cairo is that they be destroyed, according to the consensus of the righteous forefathers [Salaf], because they are new under Islam, and Cairo is a new city whose original inhabitants were Muslim; there were no churches in it previously.
As for churches in Upper Egypt, which may have been in existence before the Islamic conquest of Egypt, these may remain but may never be renovated or fixed.
The Islamic state cleric cited medieval jurist Ibn Taymiyya (d. 1328), some of whose fatwas deal with Islam’s views on churches which are described as “worse than bars and brothels.” And in fact, Taymiyya and many other jurists (such as Ibn Qayyim) called for the destruction of all churches built after the conquests (see Crucified Again, pgs. 35-36 for a review of the relevant fatwas/teachings).