"Declare war upon those to whom the Scriptures were revealed but believe neither in God nor the Last Day" (Sura 9.29).
Mohammad was a warlord and as a result many passages in the Koran have to do with war. Now you may not like the description of the Prophet as a warlord, but you must agree with me that many passage in the Koran relate to war. Mohammad spread Islam through war, through violence, and now many Muslims, who some people describe as radicals, are attempting to emulate his success by using his methods.
The passage I quoted above might be understood by some as a reference to atheists ("... but believe neither in God nor the Last Day"), but is it not really an attack on those who had once accepted the Koran but now rejected it? My understanding is that this was actually an attack on those Arabs who had reverted to paganism. This passage then can be taken, and is being taken, as an excuse to kill apostates. When violent men, read the Koran, they find many such passages. It doesn't matter that there are a small number of verses that can be read as peaceful in tenor, they are vastly outnumbered by the violent ones. The other thought I have is that perhaps the Koran is making some people violent.
Yes, i will agree they refer to war.
But war is not always bad. These are all for self-defense against people who try and kill you.
Funny how you quote out of context,
“[And] fight against those who – despite having been vouchsafed revelation [aforetime] – do not [truly] believe either in God or the last Day, and do not consider forbidden that which God and His Apostle have forbidden, and do not follow the religion of truth [which God has enjoined upon the],
till they [agree to] pay the exemption tax with a willing hand, after having been humbled [in war]” 9:29 Asad’s Translation
2. “Fight those people of the Book (Jews and Christians) who do not believe in Allah and the Last Day, do not refrain from what has been prohibited by Allah and His Rasool and do not embrace the religion of truth (Al-Islam),
until they pay Jizya (protection tax) with their own hands and feel themselves subdued.” 9:29 Malik’s Translation
3. “Fight those who believe not in Allah nor the Last Day nor hold that forbidden which hath been forbidden by Allah and His apostle nor acknowledge the religion of truth (even if they are) of the People of the Book
until they pay the Jizya with willing submission and feel themselves subdued.” 9:29 Yusuf Ali’s Translation
4. “Fight against such of those who have been given the Scripture as believe not in Allah nor the Last Day, and forbid not that which Allah hath forbidden by His messenger, and follow not the religion of truth,
until they pay the tribute readily, being brought low.” 9:29 Pickthall’s Translation
5. “Fight against those who believe not in Allâh, nor in the Last Day, nor forbid that which has been forbidden by Allâh and His Messenger and those who acknowledge not the religion of truth (i.e. Islâm) among the people of the Scripture (Jews and Christians),
until they pay the Jizyah with willing submission, and feel themselves subdued.” 9:29 Muhsin Khan’s Translation
6. “Fight those People of the Book who do not believe in Allah, nor in the Last Day, and do not take as unlawful what Allah and His Messenger have declared as unlawful, and do not profess the Faith of Truth; (fight them)
until they pay jizyah with their own hands while they are subdued.” 9:29 Mufti Taqi Usmani’s Translation
7. “Fight those who do not believe in Allah or in the Last Day and who do not consider unlawful what Allah and His Messenger have made unlawful and who do not adopt the religion of truth from those who were given the Scripture – [fight]
until they give the jizyah willingly while they are humbled.” 9:29 Sahih International Translation
This is probably the most misinterpreted verse.
The historical background of this verse was that it got revealed to the prophet (SAW) when it was a time of war between the Arab Pagans and the Muslims. And so Allah gave the Muslims permission to fight the pagans in self-defense. As for the Jizya, Non-Muslims were required to pay those since they got the benefits of practicing their believes freely, and not fighting on the Muslim side during war.
This verse is self-defense against people that are against you and in a time of war.