So Shahin Bhai in short argues that the Islamic Tradition doesn't indoctrinate people.

1. Quranic critique of emulating ancestors.

2. Critical analysis of verses by Mufasirun like Ibn Kathir.

After which he addresses the potential objections with brevity.
The verses pertaining to "we hear and we obey" have to do with personal rituals and issues of Ghaib. It's not about how the academic pursuits of Muslims or his worldly engagements.

Shahin bhai also brings to light Shaykh Abd Al-Fattah Al Ghouda's critique of mystics—
Who discourage their followers from thinking critically. Shaykh Ghouda quite explicitly states that these mystics have deviated from the Islamic Tradition.
Overall the article is a good short read and an introduction to the Islamic concept of Critical Engagement.

Additional thoughts in further replies.
So the main polemical thrust against Muslims is that we indoctrinate our Children from early on and they never learn to think critically throughout the period of their lives.

The problem is that the skeptic assumes that he isn't indoctrinated with certain metaphysical axioms.
The key among them is this:

If it isn't empirically observable, it doesn't exist.

It seems like an honest approach but they aren't consistent about it and they have a shallow perspective of "empiricism".
It barely registers on them that they don't empirically observe every claim made by the scientists and simply trust that they are making accurate assessments and analysis.

They don't analyze every issue for themselves.

This is most apparent in the now out of fashion—
New Atheist movement who merely run with some sloganeering bullet points against religion and the religious.

They ignore the fact that largely their axioms and observations of their "priests" browbeaten in their ranks. And if anyone even questions their axioms it is met with—
Derision and mockery.

So it's not as if atheists are immune to being indoctrinated into certain cult like tendencies.
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