There are many Churches in present day Muslim countries e.g. Egypt, Syria, Turkey, Pakistan, and Indonesia. This is in line with the freedom of religion given in Islam.
However it is right to note that some countries have gone against this Islamic injunction and prohibited collective worship by non-Muslims. This is wrong and completely unacceptable. Never did the Prophet Muhammad(sa) forbid the building of a church, nor did he order the demolition of a church. In fact the Holy Qur’an mentions that we Muslims are to defend Churches, and synagogues if they are attacked,
Those who have been driven out from their homes unjustly only because they said, ‘Our Lord is Allah’ – And if Allah did not repel some men by means of others, there would surely have been pulled down cloisters and churches and synagogues and mosques, wherein the name of Allah is oft-commemorated. And Allah will surely help one who helps Him. Allah is indeed Powerful, Mighty. (Holy Qur’an, Ch.22:V.41)