Let's look at some Islamic apologist arguments about how the Quran promotes progressive values, reason and freedom of thought.
Myth #1: Quran encourages free thinking
The myth of Quran promoting free thought is busted by looking at some specific verses in the Quran.
Quran 4:59 to 4:64 - O you who have believed, obey Allah and obey the Messenger and those in authority among you. And if you disagree over anything, refer it to Allah and the Messenger, if you should believe in Allah and the Last Day. That is the best [way] and best in result. Have you not seen those who claim to have believed in what was revealed to you, [O Muhammad], and what was revealed before you? They wish to refer legislation to Taghut, while they were commanded to reject it; and Satan wishes to lead them far astray. And when it is said to them, "Come to what Allah has revealed and to the Messenger," you see the hypocrites turning away from you in aversion. So how [will it be] when disaster strikes them because of what their hands have put forth and then they come to you swearing by Allah , "We intended nothing but good conduct and accommodation." Those are the ones of whom Allah knows what is in their hearts, so turn away from them but admonish them and speak to them a far-reaching word. And We did not send any messenger except to be obeyed by permission of Allah. And if, when they wronged themselves, they had come to you, [O Muhammad], and asked forgiveness of Allah and the Messenger had asked forgiveness for them, they would have found Allah Accepting of repentance and Merciful.
As you can see, the Quran repeatedly demands obedience to authority on the face of any disagreements without entertaining free thought. Let's read on further.
Quran 4:65 - But no, by your Lord, they will not [truly] believe until they make you, [O Muhammad], judge concerning that over which they dispute among themselves and then find within themselves no discomfort from what you have judged and submit in [full, willing] submission.
Notice how the Quran makes it abundantly clear that believers won't be considered true believers unless the submit to the authority of Muhammad without the slightest discomfort or disagreement. But it gets worse.
Quran 4:66 to 4:69 - And if We had decreed upon them, "Kill yourselves" or "Leave your homes," they would not have done it, except for a few of them. But if they had done what they were instructed, it would have been better for them and a firmer position [for them in faith]. And then We would have given them from Us a great reward. And We would have guided them to a straight path. And whoever obeys Allah and the Messenger - those will be with the ones upon whom Allah has bestowed favor of the prophets, the steadfast affirmers of truth, the martyrs and the righteous. And excellent are those as companions.
The Quran demands obedience even if the command given to believers were to "kill yourselves" or "leave your homes" as the Quran clearly puts it!
Quran 4:80 - He who obeys the Messenger has obeyed Allah ; but those who turn away - We have not sent you over them as a guardian.
Let's look carefully at the above statement. It doesn't simply say obey Allah and Muhammad. It instead says that whoever obeys Muhammad is thereby obeying Allah. This simply reinforces the idea that Muhammad indeed is practically the authority in Islam.
Quran 33:21 - There has certainly been for you in the Messenger of Allah an excellent pattern for anyone whose hope is in Allah and the Last Day and [who] remembers Allah often.
The above verse makes it clear that Muhammad is a role model or an example to be imitated for the believers. Remember, not merely an inspiration but an example to be followed.
Now, let's check another part of the Quran to see its stance on doubtful questioning from believers.
Quran 5:101 to 5:102 - O you who have believed, do not ask about things which, if they are shown to you, will distress you. But if you ask about them while the Qur'an is being revealed, they will be shown to you. Allah has pardoned that which is past; and Allah is Forgiving and Forbearing. A people asked such [questions] before you; then they became thereby disbelievers.
The Quran discourages believers from asking questions about things which can potentially cause themselves distress. It mentions that some people who asked such questions became disbelievers because of that.
And what might be the purpose of life according to Islam?
Quran 51:56 - And I did not create the jinn and mankind except to worship Me.
The reason why Allah has created us as per the Quran is nothing else than to worship him. Sounds like somebody creating robots to sing his praises.
Quran 49:14 to 49:15 - The bedouins say, "We have believed." Say, "You have not [yet] believed; but say [instead], 'We have submitted,' for faith has not yet entered your hearts. And if you obey Allah and His Messenger, He will not deprive you from your deeds of anything. Indeed, Allah is Forgiving and Merciful." The believers are only the ones who have believed in Allah and His Messenger and then doubt not but strive with their properties and their lives in the cause of Allah. It is those who are the truthful.
Quran in the above verses encourages blind submission (islam) and obedience even in the absence of belief (iman). To become true believers, it is stated that there should be no doubt in Islam.
Myth #2: Kufr doesn't mean disbelief; disbelievers don't get hellfire
Quran 40:70 to 40:72 - Those who deny the Book and that with which We sent Our messengers - they are going to know, When the shackles are around their necks and the chains; they will be dragged In boiling water; then in the Fire they will be filled [with flame].
The above verses are clear that denying the Quran and its messages (with which the messengers were previously sent forth) is going to land people in hellfire.
Quran 48:13 - And whoever has not believed in Allah and His Messenger - then indeed, We have prepared for the disbelievers a Blaze.
In the above verse, the word kufr (which liberal Muslims often say doesn't refer to disbelief) is clearly associated with the action of not believing in Allah and Muhammad. And for such people, hellfire is clearly assigned by Allah.
Quran 5:72 - They have certainly disbelieved who say, "Allah is the Messiah, the son of Mary" while the Messiah has said, "O Children of Israel, worship Allah, my Lord and your Lord." Indeed, he who associates others with Allah – Allah has forbidden him Paradise, and his refuge is the Fire. And there are not for the wrongdoers any helpers.
The above verse clearly states that those who associate others with Allah (i.e. don't accept Tawheed or strict monotheism) are going to hellfire.
Quran 3:151 - We will cast terror into the hearts of those who disbelieve for what they have associated with Allah of which He had not sent down [any] authority. And their refuge will be the Fire, and wretched is the residence of the wrongdoers.
Again the Quran reiterates that people who associate others with Allah will be made to feel terror because of associating partners with Allah.
Quran 47:8 to 47:10 - But those who disbelieve - for them is misery, and He will waste their deeds. That is because they disliked what Allah revealed, so He rendered worthless their deeds. Have they not traveled through the land and seen how was the end of those before them? Allah destroyed [everything] over them, and for the disbelievers is something comparable. That is because Allah is the protector of those who have believed and because the disbelievers have no protector. Indeed, Allah will admit those who have believed and done righteous deeds to gardens beneath which rivers flow, but those who disbelieve enjoy themselves and eat as grazing livestock eat, and the Fire will be a residence for them.
Disliking Allah's revelations means Allah will cause such people misery, cause their good deeds to be wasted and put them into hellfire.