Before beginning the discussion, I wish to present two important points as a preamble to some of the misconceptions.
Ibrahim ibn Wasif Shah al Katib writes:
أن القبط تنسب إلى قبطيم ابن مصرایم بن مصر بن حام بن نوح، وأن قبطيم أول من عمل العجائب بمصر وأثار بها المعادن وشق الأنهار لما ولي أرض مصر بعد أبيه مصرایم، وأنه لحق بلبلة الألسن، وخرج منها وهو يعرف اللغة القبطية ، … وقيل: بل قفط بن حام بن نوح نکح بخت بنت يتاويل بن ترسل بن یافث بن نوح، فولدت له بوقير، وقبط أبا قبط مصر … وقیل القبط من ولد قبط بن مصر بن قفط بن حام ابن نوح، وبمصر هذا سميت مصر
The Copts hail from Qibtim ibn Misrayim ibn Misr ibn Ham ibn Nuh. Qibtim was the first to do wonders in Misr [Egypt]; he worked the mines, and dug water-courses while ruling the land of Misr, after his father Misrayim. He lived until the Confusion of Tongues, and from it came the Coptic language which he knew… Another opinion is that Qift ibn Ham ibn Nuh married Bukht bint Yatawil ibn Tursil ibn Yafith ibn Nuh. Buqir and Qibt were born to her, Qibt becoming the father of Misr… Another view is that the Copts are of the children of Qibt ibn Misr ibn Qift ibn Ham ibn Nuh and that is why Misr is named Misr.
Dear reader, this makes it quite evident that the original dwellers of Egypt were the Copts. Thereafter, others such as the Arabs, the Israelites, the Greeks, and the Romans settled in Egypt. Some were of the armies that stayed back, some stayed on after arriving for business, and so on.
After Allah subhanahu wa ta ‘ala saved Nabi Nuh ‘alayh al Salam and those who were with him in the ark, He scattered his children throughout the lands. Allah subhanahu wa ta ‘ala says:
وَجَعَلْنَا ذُرِّيَّتَهُ هُمُ الْبَاقِيْنَ
And We made his descendants those remaining [on the earth].
Thereafter Nabi Nuh ‘alayh al Salam passed away and his children continued on the true faith. Shaitan came to them with the intent of leading them astray and called them to idolatry, just as he had beguiled their predecessors. Eventually, Egypt became a land of polytheism.
With the spread of polytheism and its acceptance the beliefs of people changed. In this climate there were some individuals, few and far between, who believed in the Islamic creed though they were forced to hide their faith. They were influenced by the teachings of the Prophets who had inhabited Egypt such as Yusuf, his father Yaqub, and Musa ‘alayhim al Salam. This is clearly elucidated in the Qur’an where Allah subhanahu wa ta ‘ala speaks of the pious man of faith from the house of Firoun and the advice he gave to his people:
وَقَالَ رَجُلٌ مُّؤْمِنٌ مِّنْ أٰلِ فِرْعَوْنَ يَكْتُمُ إِيمٰنَهُ أَتَقْتُلُوْنَ رَجُلًا أَن يَّقُوْلَ رَبِّىَ اللّٰهُ وَقَدْ جَآءَكُمْ بِالْبَيِّنٰتِ مِن رَّبِّكُمْ وَإِن يَّكُ كَاذِبًا فَعَلَيْهِ كَذِبُهُ وَإِن يَّكُ صَادِقًا يُصِبْكُمْ بَعْضُ الَّذِىْ يَعِدُكُمْ إِنَّ اللّٰهَ لَا يَهْدِىْ مَنْ هُوَ مُسْرِفٌ كَذَّابٌ يٰقَوْمِ لَكُمُ الْمُلْكُ الْيَوْمَ ظٰهِرِيْنَ فِى الْأَرْضِ فَمَن يَّنْصُرُنَا مِنْۢ بَأْسِ اللّٰهِ إِنْ جَآءَنَا قَالَ فِرْعَوْنُ مَآ أُرِيْكُمْ إِلَّا مَآ أَرٰى وَمَآ أَهْدِيْكُمْ إِلَّا سَبِيْلَ الرَّشَادِ وَقَالَ الَّذِىٓ أٰمَنَ يٰقَوْمِ إِنِّىٓ أَخَافُ عَلَيْكُم مِّثْلَ يَوْمِ الْأَحْزَابِ مِثْلَ دَأْبِ قَوْمِ نُوْحٍ وَّعَادٍ وَّثَمُوْدَ وَالَّذِيْنَ مِنْۢ بَعْدِهِمْ وَمَا اللّٰهُ يُرِيْدُ ظُلْمًا لِّلْعِبَادِ وَيٰقَوْمِ إِنِّىٓ أَخَافُ عَلَيْكُمْ يَوْمَ التَّنَادِ يَوْمَ تُوَلُّوْنَ مُدْبِرِيْنَ مَا لَكُم مِّنَ اللّٰهِ مِنْ عَاصِمٍ وَمَن يُّضْلِلِ اللّٰهُ فَمَا لَهُ مِنْ هَادٍ وَلَقَدْ جَآءَكُمْ يُوْسُفُ مِنْ قَبْلُ بِالْبَيِّنٰتِ فَمَا زِلْتُمْ فِىْ شَكٍّ مِّمَّا جَآءَكُمْ بِهِ حَتَّىٰٓ إِذَا هَلَكَ قُلْتُمْ لَن يَّبْعَثَ اللّٰهُ مِنْۢ بَعْدِهِ رَسُوْلًا كَذٰلِكَ يُضِلُّ اللّٰهُ مَنْ هُوَ مُسْرِفٌ مُّرْتَابٌ
And a believing man from the family of Pharaoh who concealed his faith said, “Do you kill a man [merely] because he says, ‘My Lord is Allah,’ while he has brought you clear proofs from your Lord? And if he should be lying, then upon him is [the consequence of] his lie; but if he should be truthful, there will strike you some of what he promises you. Indeed, Allah does not guide one who is a transgressor and a liar. And he who believed said, “O my people, indeed I fear for you [a fate] like the day of the companies. Like the custom of the people of Nuh and of ‘Ad and Thamud and those after them. And Allah wants no injustice for [His] servants. And O my people, indeed I fear for you the Day of Calling. The Day you will turn your backs fleeing; there is not for you from Allah any protector. And whoever Allah sends astray – there is not for him any guide. And Joseph had already come to you before with clear proofs, but you remained in doubt of that which he brought to you, until when he died, you said, ‘Never will Allah send a messenger after him.’ Thus does Allah leave astray he who is a transgressor and sceptic.
However, most were polytheists and remained such until Christianity spread in Egypt and became the state religion.
Thus, the Copts remained as Christians until Allah subhanahu wa ta ‘ala sent Muhammad salla Llahu ‘alayhi wa sallam as the seal of Prophets to all of humanity. He abrogated all other beliefs and invited all to the faith of Islam. There were those who accepted and those who rejected. And then there were those who responded in a beautiful manner, such as Muqawqis, the King of the Copts who had gifted Mariyah al Qibtiyyah to Rasulullah salla Llahu ‘alayhi wa sallam. Rasulullah salla Llahu ‘alayhi wa sallam had given the glad tidings of the Egyptian conquest to the Sahabah radiya Llahu ‘anhum before his passing and advised them to deal with the people of Egypt in a good manner. As Allah willed, it was conquered during the reign of ‘Umar ibn al Khattab radiya Llahu ‘anhu, with his consultation, under the command of the magnanimous Companion, ‘Amr ibn al ‘As radiya Llahu ‘anhu. Thus, Egypt became an Islamic state through the grace of Allah. For this great achievement we first express our gratitude to Allah subhanahu wa ta ‘ala and then to ‘Amr ibn al ‘As radiya Llahu ‘anhu for his unyielding faith, bravery, intellect, and military prowess.
The Muslims conquered Egypt during the caliphate of ‘Umar ibn al Khattab radiya Llahu ‘anhu at the behest of ‘Amr ibn al ‘As radiya Llahu ‘anhuma due to various considerations. Amongst the considerations were the following:
In fulfilling the responsibility of preaching and calling to Allah in accordance with the divine injunction:
يٰأَيُّهَا الرَّسُوْلُ بَلِّغْ مَآ أُنْزِلَ إِلَيْكَ مِنْ رَّبِّكَ وَإِنْ لَّمْ تَفْعَلْ فَمَا بَلَّغْتَ رِسَالَتَهُ وَاللّٰهُ يَعْصِمُكَ مِنَ النَّاسِ إِنَّ اللّٰهَ لَا يَهْدِىْ الْقَوْمَ الْكٰفِرِيْنَ
O Messenger, announce that which has been revealed to you from your Lord, and if you do not, then you have not conveyed His message. And Allah will protect you from the people. Indeed, Allah does not guide the disbelieving people.
In order to create an Islamic discipline and lifestyle that covers the entire land of Allah; amongst it the land of Egypt. Allah subhanahu wa ta ‘ala says:
هُوَ الَّذِىْ أَرْسَلَ رَسُوْلَهُ بِالْهُدٰى وَدِيْنِ الْحَقِّ لِيُظْهِرَهُ عَلَى الدِّيْنِ كُلِّهِ وَلَوْ كَرِهَ الْمُشْرِكُوْنَ
It is He who has sent His Messenger with guidance and the religion of truth to manifest it over all religion, although they who associate others with Allah dislike it.
And Allah says:
وَمَآ أَرْسَلْنَاكَ إِلَّا رَحْمَةً لِّلْعَالَمِيْنَ
And We have not sent you, [O Muhammad], except as a mercy to the worlds.
The Muslims understood the concern of Rasulullah salla Llahu ‘alayhi wa sallam to be their concern. This was eloquently elucidated by Rabi’ ibn ‘Amir radiya Llahu ‘anhu addressing Rustam, the Persian general:
ان الله ابتعثنا لنخرج العباد من عبادة العباد إلى عبادة الله الواحد القهار ومن جور الأديان إلى عدل الإسلام
Allah has sent us to bring mankind out of worship of mankind to the worship of Allah and from the oppression of religions to the justice of Islam.
This was the exact words by which ‘Ubadah ibn Samit radiya Llahu ‘anhu addressed Muqawqis, the King of the Copts.
It had become all the more vital, now, to expel the occupying Roman forces from Egypt and North Africa to prevent enemy attacks on the Levant and Arabian Peninsula from the southern and western regions. This would also effectively bar the enemy from crossing the Egyptian, Alexandrian, and Libyan borders and attacking the Islamic Levant. Further, Egypt would serve as a base in conquering Spain and beyond.
As a realization of the prophecy of Nabi Muhammad salla Llahu ‘alayhi wa sallam:
إنكم ستفتحون مصر وهي أرض يسمى فيها القيراط فإذا فتحتموها فأحسنوا إلى أهلها فإن لهم ذمة ورحماً
You would soon conquer Egypt and that is a land in which the Qirat is used. So when you conquer it, treat its inhabitants well. For they have upon you the right of protection in view of the blood-relation or relationship of marriage you have with them.,
 Al Mawa’iz, vol. 3 pg. 257. The scholars have differed with regards to the reason Misr was called Misr. hereunder are some of the views:
 Surah al Saffat: 77.
 Al Mawa’iz wa al I’tibar, vol. 4 pg. 389.
 Surah Ghafir: 28-34.
 Tarikh ibn Khaldun, vol. 2 pg. 89.
 Surah al Ma’idah: 67.
 Surah al Tawbah: 33.
 Surah al Ambiya’: 107.
 Sahih Muslim: 2543.
 Dr Jamal ‘Abdul Hadi: Fath Misr, pg. 29.