The ability to think for oneself might, as you say, indeed be innate - yet, the point being made here is that the oppressive dynamics reigning in education and many other aspects of society, manage very well to extinguish every spark of this ability trying to flare up.
I also take note of the contradiction in your statement that the faculty of independent thought is innate, yet "some can and others cannot."
The idea is to prove you both right and wrong. Right, because a faculty of self-realisation through independence of thought is indeed believed to be innate - and wrong because there are none who can't, there are only those who haven't had the good luck to see this faculty freed from the oppression it is being constrained by - QED.