The Holy verse says:
" And as for those who disbelieved, I will punish them with a severe punishment in this world and the Hereafter, and they will have no helpers." (3:56)
Who is Punishing ?
Actually I was amazed why is this verse considered a violent verse. Is God ordering the Muslims here to punish the disbelievers themselves? actually NO. The only ONE who has the right to punish or forgive is GOD ALONE and that verse emphasizes that. GOD said "I will punish" NOT "YOU will punish" so where is the call to violence here?.
Why the warning ?
The verse here is giving a warning to the disbelievers that if you continue being a disbeliever then God will punish you during your life time and in the afterlife. This warning is meant to make them reconsider their attitude and think again. It is actually because of God's mercy, He wants to warn them like when you warn your son not to do something because the consequences are really bad.
Let's take a deeper look in the verse and we can easily conclude the following:
1- The verse is an evident proof that every human is FREE to choose his way, In Islam "there is no compulsion in religion" (2:256). This is a fundamental concept in Islam, you make your choice but remember you will have to face the consequences of your choice.
2- Muslims are NOT allowed to play the punisher to anyone even those who do not believe in God. Again this is another fundamental concept in Islam. We do not have the right to judge or punish each other. Like in the verse " Indeed, those who have believed and those who were Jews and the Sabeans and the Christians and the Magians and those who associated with Allah – Allah will judge between them on the Day of Resurrection. Indeed Allah is, over all things, Witness." (22:17)
So judging and punishing is in the hands of God ONLY. This is a proof of how just Islam is. Muslims are not allowed to punish even those who associated others with GOD. This is actually a point both Muslims and non-Muslims must understand.
3- Threatening the disbeliever is a merciful act from a merciful God. GOD does not want to punish anyone so He is warning those transgressing that this will make them liable to punishment so they can repent for their own good. If they believed in God, it is for their own sake, their believing is not going to increase GOD's kingdom and their disbelieving will not decrease it. Like when you threaten you child when he is doing something that can harm him, you personally will not be affected but you do not want him hurt so you threaten him may be he will reconsider his behavior when you face him with the inevitable consequences of his deeds.
4- If someone is a disbeliever, he does not believe in the existence of God in the first place, so why will he be so much offended by this verse. If someone does not believe in God then he does not believe in heaven or hell then he should not be affected by this verse or any other verse conveying the same message. So that person should not look at the verse as a violent verse as he does not believe in being judged for his deeds in the first place.
5- If someone is a believer in God, but not a Muslim, then he will surely find in his religion whatever it is similar verses, because religions oblige you to consider the consequences of your deeds. Religions raise the voice of conscience in their followers by making them understand that whatever you do you will be rewarded or punished accordingly. So again I am amazed why will they consider such a verse violent?