“As to those who reject faith, I will punish them with terrible agony in this world and in the Hereafter, nor will they have anyone to help.” – Quran 3:56
This verse references God’s wrath on the people who disbelieved in Jesus. The passage does not endorse Muslims to commit violence. Here, read the entire passage in its context,
3:55 [Mention] when God said, “O Jesus, indeed I will take you and raise you to Myself and purify you from those who disbelieve and make those who follow you [in submission to God alone] superior to those who disbelieve until the Day of Resurrection. Then to Me is your return, and I will judge between you concerning that in which you used to differ.
3:56 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.”
3:57 But as for those who believed and did righteous deeds, He will give them in full their rewards, and God does not like the wrongdoers.
Quran Commentary on 3:56
Sayyid Abul Ala Maududi – Tafhim al-Qur’an – The Meaning of the Qur’an
51 The word (mutawaffi) in the Arabic text is from (tawaffa) which literally means “to take and to receive” and “to seize the soul” is not its lexical but metaphorical meaning. Here it means “to recall from mission.” Allah recalled Jesus because the Israelites had rejected him in spite of the clear Signs he had brought. They had been disobeying God for centuries and, in spite of many a warning and admonition served to them, their national character was rapidly deteriorating. They had killed several Prophets, one after the other, and had grown so audacious as to demand the blood of any good man who ventured to invite them to the Right Way. In order to give them the last chance for turning to the Truth, God appointed among them two great Prophets, Jesus and John (God’s peace be upon them), at one and the same time. These Prophets came with such clear signs of their appointment from Allah that only such people dared reject them as were utterly perverted and prejudiced against the Truth and were averse to following the Right Way. Nevertheless the Israelites lost their last chance also as they not only rejected their invitation but also had the head of a great Prophet like John cut off openly at the request of a dancing girl. ‘And their Pharisees and Jurists conspired and sought to get Jesus punished with the death sentence by the Roman Government. Thus they had proved themselves to be so obdurate that it was useless to give the Israelites any further chance. So Allah recalled His Prophet Jesus and inflicted on them a life of disgrace up to the Day of Resurrection.
It will be useful here to bear in mind the fact that this whole discourse is meant to refute and correct the Christian belief in the God-head of Jesus. Three main things were responsible for the prevalence of this belief among the Christians:
(1) The miraculous birth of Jesus.
(2) His concrete and tangible miracles.
(3) His ascension to heaven about which their Scriptures were explicit.
The Qur’an confirmed the first thing and made it plain that the birth of Jesus without a father was only a manifestation of the infinite powers of Allah. He can create anybody in whatever manner He wills. His miraculous birth, therefore, is no reason why he should be made a god or a partner in Godhead.
The Qur’an also confirms the second thing and even recounts the miracles performed by Jesus, but makes it clear that all those miracles were performed by him, as a servant of Allah, by His leave and not as an independent authority. It is, therefore, wrong to infer that Jesus was a partner in Godhead.
Now let us consider the third thing. If the Christian belief in “Ascension” had been wholly baseless, it could have been refuted by pointing out that the object of their worship, the so-called “Son of God”, expired long ago and had become one with dust, and that they could see, for their full satisfaction, his grave at such and such a place. But the Qur’an does not declare this explicitly. On the other hand, it not only uses such words as give at least a vague suggestion of his “Ascension”, but also denies that Jesus was crucified at all. According to it the one who gave a loud cry at his last hour, saying, “Eli” Eli, lama sabachthani?” and the one whose picture they carry on the cross, was not Messiah at all, because God had recalled to Himself the real Messiah before the crucifixion took place.
It is thus clear that those people who try to prove the death of Jesus from these verses, really try to show that God is not able to express Himself clearly and unambiguously. (May God protect us from such a blasphemy!)
52″Those who rejected” him were the Jews who were invited by Jesus to accept the Truth.
“Those who follow” him are really the Muslims only but if it may be taken to imply all those who believe in him, then the sincere Christians may also be included. 
 Sayyid Abul Ala Maududi – Tafhim al-Qur’an – The Meaning of the Qur’an http://www.englishtafsir.com/Quran/3/index.html#sdfootnote51sym