So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush. If they repent and keep up prayer and pay the poor-rate, leave their way free to them. ... Fight those who do not believe in Allah, nor in the Last Day, nor forbid what Allah and his Messenger have forbidden, nor follow the religion of truth, even if they are of the People of the Book [i.e., Jews and Christians], until they pay the Jizya [i.e., the special tax imposed on non-Muslims] in acknowledgment of superiority and they are in a state of subjection. And the Jews say: Uzair [i.e., Ezra] is the son of Allah; and the Christians say: the Messiah is the son of Allah. These are the blasphemous words of their mouths. They imitate the saying of those who disbelieved before. May Allah destroy them! They have surely turned away.
Robert Spencer comments:
Thus, the difference between the Qur'an's "slay the unbelievers wherever you find them" (Sura 9:5) and the Bible verses he quotes is that in Islam, violence is not justified by twisting a few scattered verses; instead, it's enshrined in tradition and theology.
Dr. Muhammad Muhsin Khan, translator of the Hadith collection Sahih Bukhari, explains that the Qur'an's violent verses actually take precedence over its peaceful ones: "At first 'the fighting' was forbidden, then it was permitted and after that it was made obligatory." S. K. Malik in The Qur'anic Concept of War explains that Allah gave Muslims "a divine command making war a religious obligation for the faithful." All four schools of Sunni Muslim jurisprudence -- Shafi'i, Maliki, Hanafi, and Hanbali -- teach an elaborate doctrine of jihad that sanctions killing in the name of Islam. Said the great Muslim jurist, philosopher, and historian Ibn Khaldun (d. 1406): "In the Muslim community, the holy war is a religious duty, because of the universalism of the [Muslim] mission and [the obligation to] convert everybody to Islam either by persuasion or by force. The other religious groups did not have a universal mission, and the holy war was not a religious duty for them, save only for purposes of defense... Islam is under obligation to gain power over other nations."
This is the triple choice: conversion, death, or submission. This verse comes from Sura At-Tawba, the last sura revealed. If any verse contradicts it, Sura 9:29 must be given precedence because the sura from which it comes is the Qur'an’s last word on the subject. Even if the tolerance verses aren't cancelled according to the Muslim principle of abrogation (naskh), the tolerant verses such as those you quote must be understood in light of Sura 9.
I didn’t make up this interpretation. It comes from respected Islamic authorities: Ibn Kathir, Ibn Juzayy, Tafsir al-Jalalayn, and innumerable other classic and respected Qur’an commentaries. And they were working from the Muhammad’s amplification of the triple alternative for unbelievers -- conversion, death, or submission -- in a strong Hadith in Sahih Muslim (4294).