You have it backward; study after study done on the subject of Islamic extremists and why they join extremist groups shows that the majority lack even a basic understanding of Islam. While it's true that many of the leaders of these organizations are well versed in Islam, they only use their extensive knowledge of Islam to deceive those who are ignorant in order to get them to join their ranks and carry out atrocities in the name of Islam.
From the UN:
UN study finds foreign fighters in Syria 'lack basic understanding of Islam'
“Most saw their religion in terms of justice and injustice rather than in terms of piety and spirituality,” said the authors of the report, which was based on interviews with 43 people from 12 countries.
“Religious belief seems to have played a minimal role in the motivation of this sample,” the report found, saying economic factors had become more important as terrorist groups promised wages, homes and even wives.
From MI5 in the UK:
Research, carried out by MI5's behavioural science unit, based on in-depth case studies on "several hundred individuals known to be involved in, or closely associated with, violent extremist activity" ranging from fundraising to planning suicide bombings in Britain found that far from being religious zealots, a large number of those involved in terrorism do not practise their faith regularly. Many lack religious literacy and could actually be regarded as religious novices. Very few have been brought up in strongly religious households, and there is a higher than average proportion of converts. Some are involved in drug-taking, drinking alcohol and visiting prostitutes. MI5 says there is evidence that a well-established religious identity actually protects against violent radicalisation.
In the Philippines:
Cocoy Tulawie, a politician and member of an influential family in Sulu, said this has long been the norm and local government officials have been in connivance with Abu Sayyaf for decades.
He said younger members are ignorant of Islam, yet they are extremely fanatical about representing it. Their version of Islam is flawed simply because the dawas - or Islamic schools - are usually in the main towns and they do not get the chance to study the Quran "properly".
That ignorance, he said, is what makes them dangerous.
And a couple more reports:
Thousands of leaked Islamic State documents reveals most of its recruits from its earliest days came with only the most basic knowledge of Islam. A little more than 3,000 of these documents included the recruits’ knowledge of Shariah, the system that interprets into law verses from the Quran and “hadith” — the sayings and actions of the Prophet Muhammad.
According to the documents, which were acquired by the Syrian opposition site Zaman al-Wasl and shared with the AP, 70 percent of recruits were listed as having just “basic” knowledge of Shariah — the lowest possible choice. Around 24 percent were categorized as having an “intermediate” knowledge, with just 5 percent considered advanced students of Islam.
The group preys on this religious ignorance, allowing extremists to impose a brand of Islam constructed to suit its goal of maximum territorial expansion and carnage as soon as recruits come under its sway.
From Cradle to Grave: The Lifecycle of Foreign Fighters in Iraq and Syria
Combating Terrorism Center at West Point United States Military Academy
Less than 15% of fighters coded by religious background had any formal religious education. Additionally, individuals who made the decision to become a foreign fighter tended not to be lifelong strict adherents to Islam, but also rarely appeared to be recent converts. Those who were Muslims since childhood (but not overly religious), as well as those who were converts (but not too recent), were well-represented in the data.
One other way to parse out the role of religion is to try to assess the level of each fighter’s religious education. In an attempt to code religious education, we asked coders to code both formal types of religious education (at a madrasa or other religious institute of higher education) as well as informal types (indications that they had been part of a study group or sought religious guidance at a local mosque). Much like the data related to the coding of an individual’s conversion to the Islamic faith, the sample in the case of religious education was also very small (n = 203). The results of this breakdown can be seen in Figure 3.9, which shows that a small minority of the foreign fighters had any formal religious education (less than 15%), while the majority of them had no religious guidance (or just basic guidance) before their travel.
Both findings indicate that the majority of the foreign fighters had limited familiarity with the tenets of the Islamic faith. This is consistent with the findings from the CTC’s earlier report, which showed that very small numbers of foreign fighters reported having any religious education and that approximately 70% of fighters reported having a basic knowledge of Shari`a law.
Given these findings, it seems that the ability of the foreign fighters to develop an emotional and cognitive attachment to the jihadi community is based on other factors, which may be more related to cultural and political dimensions of their identities as Muslims in non-Muslim societies than religious triggers. The ability of jihadi groups to recruit foreign fighters is thus based on creating a narrative that is focused on the ongoing deprivation of Muslims, both in specific Western polities, as well as in the international arena. While convincing them that joining the jihadi movement based on specific religious imperatives may be important, it seems to play a secondary role. Moreover, our findings also correspond with primary sources indicating that jihadi groups in general prefer to recruit individuals who have limited religious education since they are less capable of critically scrutinizing the jihadi narrative and ideology, in addition to being less familiar with contrasting Islamic schools of thought.
While it is difcult to ascertain whether the recruiter or potential foreign fighter initiates the connection, it seems that religious figures play a relatively minimal role in this process, a fact that provides support for previous findings indicating that political and cultural aspects of jihadi ideology play a greater role in the radicalization of foreign fighters than strictly religious ones.
As can be seen in the above articles, Most recruits of Islamic extremists groups are not well versed in Islam and ignorance of Islam is a common theme.
The Muslims that were being spoken to in the Qur'an lived in a different culture, at a different point in time, and were facing unique situations. You can't read the Qur'an from a modern perspective, you have to read it through a historical lens, if not, you will continue to misinterpret what it's saying.
The violent verses found in the Qur'an don't abrogate the verses of peace because of the context they were written in. There are certain situations where the verses of peace apply, and others where the verses of violence apply, therefore, each verse has a specific context and application. In other words, each verse in the Qur'an is to be applied to its appropriate situation. For example, when Qur'an 9:5 says
"When the Sacred Months have passed, kill the polytheists wherever you find them. And capture them, and besiege them, and lie in wait for them at every ambush," it is dealing with a specific event at a point in history when Meccan pagans were breaking their peace treaties and declaring war on the Muslims, so that verse would not negate the peaceful verses in the Qur'an since it is very specific to it's intent and the point in history it was to be applied.
Textual and historical context are key to interpreting religious scriptures, and if someone reads them without knowing the backstory, they will almost certainly misinterpret their true meaning.
Muhammad and his companions were warriors. If we look at Muhammad and his actions through a historical lens, while they appear bad from our modern perspective, they were normal for the point in history at which he lived. In other words, he was no worse than anyone else who was in a position of leadership in his day, whether they be Jew, Christian, Muslim, or Pagan.
The verses found in the Qur'an were revealed during specific battles that took place during the 7th century. There's not a command found anywhere in the Qur'an that instructs Muslims to kill non-believers forever; once the battles during the days of Muhammad were over, that was it. That point in history and those being spoken to have long passed, and the verses commanding that unbelievers be killed or converted to Islam are no longer applicable to Muslims today.
Since there aren't millions of Muslims going around killing people, we know this statement isn't true. If Islam taught as you believe it does, there would be countless Muslims taking whatever weapons they could get their hands on to kill non-believers every single day in every corner of the globe. This is not happening. Instead, what we see is Muslims living in peace and harmony with their neighbors, working and playing together with non-Muslims, fighting against violence and extremism in tandem with non-Muslims, and working alongside non-Muslims in their communities to address poverty, homelessness, and other injustices through charitable giving and advocacy.