I have read that
most Muslim schools focus on rote memorization of religious texts and
discourage independent thinking. In other words, the students are required
to memorize passages from religious books, but they are not allowed to learn
about modern scientific ideas such as evolution, history of nations compiled
by secular historians, or anything which would conflict with the religious
tenants of Islam. Some of the religious schools merely propagandize militant
Islamic beliefs and indoctrinate little boys into becoming warriors for the
next Jihād. Is it because Islam itself discourages intellectual activity?
Does Islam really permit critical thinking?

Answer:

I would rather say
that Islam encourages critical thinking instead of just permitting it. At
scores of places in the Holy Qur’ān, the Almighty has exhorted man to think
about the signs that are spread around him and that testify to the greatness
of Allah. The Holy Qur’ān reads:

None
will grasp the message but men of intellect? (2:269)

Most
certainly the worst of animals in Allah’s sight are the deaf, the dumb who
do not use their brains. (8:22)

Behold in the creation of the heavens and the alteration of night and day,
there are indeed signs for men of intellect. (3:190)

We are not supposed to
close our eyes and live this life being obsessed with worldly pleasures as
animals who only know how to strive for their bodily desires. We are rather
supposed to ponder, deliberate and choose a proper course of action for
whatever undertaking we venture. Thus, critical thinking is not confined to
thinking about the stars and the moon. It is rather moving ahead in every
field of science and arts. The discoveries that we succeed to make in these
fields will evidently guide us how to appreciate the Original Creator of
everything, who always partake in our lives like a concerned and active
Mentor.