If according to Quran, Allah does not charge a soul except [with that within] its capacity then why people die out of pain?

لاَ يُكَلِّفُ اللَّهُ نَفْسًا إِلاَّ وُسْعَهَا

(Allah burdens not a person beyond his scope)

Means, Allah does not ask a soul what is beyond its ability. This only demonstrates Allah's kindness, compassion and generosity towards His creation. This Ayah is the Ayah that abrogated the Ayah that worried the Companions, that is, Allah's statement,

وَإِن تُبْدُواْ مَا فِي أَنفُسِكُمْ أَوْ تُخْفُوهُ يُحَاسِبْكُم بِهِ اللَّهُ

(And whether you disclose what is in yourselves or conceal it, Allah will call you to account for it.)

This indicates that although Allah will question His servants and judge them, He will only punish for what one is able to protect himself from. As for what one cannot protect himself from, such as what one says to himself - or passing thoughts - they will not be punished for that. We should state here that to dislike the evil thoughts that cross one's mind is a part of faith.

Source: Tafsir Ibn Kathir

The pain while death is based on you deeds. If the dying person is a Kafir the death angel will take his soul very Harshly and he have great pain. On the other a believer's soul is taken out easily and he would fell like a bite of an ant. If he was a believer and did good deeds in his lifetime Allah won't give him too much pain while death. Allah knows the best.