ISIS and Al-Qaeda are getting their facts from the Qur'an and Ahadith and distorting them. This is much like how Christianity distorted teachings of the Bible and decided that they had to fight the infidels. The crusaders were terrorists, and so are these terror groups who distort the beautiful teachings of Islam.
In Tafsir Ibn Kathir, it is stated:
Allah said,
(Fight against those who believe not in Allah, nor in the Last Day, nor forbid that which has been forbidden by Allah and His Messenger, and those who acknowledge not the religion of truth among the People of the Scripture, until they pay the Jizyah with willing submission, and feel themselves subdued.) Therefore, when People of the Scriptures disbelieved in Muhammad , they had no beneficial faith in any Messenger or what the Messengers brought. Rather, they followed their religions because this conformed with their ideas, lusts and the ways of their forefathers, not because they are Allah's Law and religion. Had they been true believers in their religions, that faith would have directed them to believe in Muhammad , because all Prophets gave the good news of Muhammad's advent and commanded them to obey and follow him. Yet when he was sent, they disbelieved in him, even though he is the mightiest of all Messengers. Therefore, they do not follow the religion of earlier Prophets because these religions came from Allah, but because these suit their desires and lusts. Therefore, their claimed faith in an earlier Prophet will not benefit them because they disbelieved in the master, the mightiest, the last and most perfect of all Prophets . Hence Allah's statement,
(Fight against those who believe not in Allah, nor in the Last Day, nor forbid that which has been forbidden by Allah and His Messenger, and those who acknowledge not the religion of truth among the People of the Scripture,) This honorable Ayah was revealed with the order to fight the People of the Book, after the pagans were defeated, the people entered Allah's religion in large numbers, and the Arabian Peninsula was secured under the Muslims' control. Allah commanded His Messenger to fight the People of the Scriptures, Jews and Christians, on the ninth year of Hijrah, and he prepared his army to fight the Romans and called the people to Jihad announcing his intent and destination. The Messenger sent his intent to various Arab areas around Al-Madinah to gather forces, and he collected an army of thirty thousand. Some people from Al-Madinah and some hypocrites, in and around it, lagged behind, for that year was a year of drought and intense heat. The Messenger of Allah marched, heading towards Ash-Sham to fight the Romans until he reached Tabuk, where he set camp for about twenty days next to its water resources. He then prayed to Allah for a decision and went back to Al-Madinah because it was a hard year and the people were weak, as we will mention, Allah willing.
War with idolaters having been dealt with in previous verses, fighting with the People of the Book is introduced with this verse. The verse refers to those People of the Book who lived in Arabia. Like the idolaters of that country, they too had been actively hostile to Islam and tried to exterminate it. Muslims were, therefore, ordered to fight them unless they agreed to live as their loyal and peaceful subjects. The Jizya, referred to in the verse, was the tax which such non-Muslims had to pay as free subjects of the Muslim State in return for the protection they enjoyed under it. Islam has ordained that in Arabia, the birthplace of Islam and its headquarters, only the People of tee Book, and not idolaters, could live as subjects by paying the Jizya, while outside Arabia all non-Muslims could live under a Muslim Government on payment of this tax. Arabia, being the cradle and center of Islam and, as it were, the citadel thereof, was to be kept free from idolaters. It should also be noted that as against Jizya which was imposed on non-Muslims, the tax imposed on Muslims is called Zakat which is a heavier tax than Jizya, and Muslimss, in addition to this tax, had to perform military service which was very hard in those days from which non-Muslims were exempt. Thus the latter in a way fared better, for they had to pay a lighter tax and were also free from military service.
The verse of the Qur'an which is unanimously referred to by all Muslim scholars stating which type of verses are in the Holy Qur'an, if the following:
3:7 He it is Who has sent down to thee the Book: In it are verses basic or fundamental (of established meaning); they are the foundation of the Book: others are allegorical. But those in whose hearts is perversity follow the part thereof that is allegorical, seeking discord, and searching for its hidden meanings, but no one knows its hidden meanings except Allah. And those who are firmly grounded in knowledge say: "We believe in the Book; the whole of it is from our Lord:" and none will grasp the Message except men of understanding.
This verse above is clear, but if you wanted more information then I can post many lengthy posts about scholars giving long explanations about the meanings of this verse alone and how it relates to explaining the categories of verses in the Holy Qur'an. What is clear is that there are verses which are clear and foundational and then there are verses which are unclear. The Qur'an is not a literal Word, it is BOTH literal and metaphorical. It has parables, stories, narrations, descriptions, predictions, etc. It has many types of discourse.
With regards to my statement that the verses of Jihad require some knowledge of those instances, I refer you to Hazrat Shah Waliyullah (ra), who wrote in his book Al-Fauz Al-Kabir, a book which explains the sciences of the commentary of the Holy Qur'an, that:
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An account of the Holy War (Jihad) has been given in chapters Al-Baqara and Al-Anfal and at some other places. The penal laws (Hudud) have been mentioned in chapters Al-Ma'ida and Al-Nur. Similarly, an account of the inheritance has been given in chapter Al-Nisa' and that of marriage and divorce in chapters Al-Baqara and Al-Nisa, and at some other places.
When this form of narration, the benefit of which is available to the whole community over, there comes an other form of narration, for example, sometimes question was put to the Holy Prophet (saw)and he gave a reply, or during an event when the believers made sacrifices of their lives as well as properties while the hypocrites showed self admiration and stinginess. God praised the believers and cursed the hypocrites holding out threats to them. Or some thing happened in which the Muslims were helped and saved from harm by the enemy. God, thus, showed favours to the Muslims and thereby reminded them of those favours. At times, a situation arose wherein a need was felt for giving a warning, a rebuke, a hint, an allusion, a command, a prohibition and denouncement. God, in this connection, revealed what pertained to it. It is, therefore, necessary for the commentator to make a mention of those stories by way of a summary.
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