And kill them wherever you overtake them and expel them from wherever they have expelled you, and fitnah is worse than killing. And do not fight them at al-Masjid al- Haram until they fight you there. But if they fight you, then kill them. Such is the recompense of the disbelievers. (2.191)
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There are some verses in Surah Tawbah [surah 9] which some people may misunderstand or take out of context;
But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for Allah is Oft-forgiving, Most Merciful.
[Qur'an Al-Tawbah Repentance 9:5]
But in context it is referring to those who are in a state of warfare with the Muslims.
For example, those who have a peace treaty with the Muslims are not fought; Except those of the polytheists with whom you have a treaty, and who have not subsequently failed you in aught, nor have supported anyone against you. So fulfill their treaty to them to the end of their term. Surely Allâh loves Al- Mattaqûn (the pious - see V.2:2).
[Qur'an 9:4]
Those who do not have a peace treaty, then it depends on the scenario - if they are peaceful with you and not a threat - then its not necessary to fight them. However, if they are likely to harm, then precautions are taken.
Okay, but still.. killing all polytheists?
Let's look at the verse that comes after the original verse [9:5]:
And if anyone of the Mushrikûn (polytheists, idolaters, pagans, disbelievers in the Oneness of Allâh) seeks your protection then grant him protection, so that he may hear the Word of Allâh (the Qur'ân), and then escort him to where he can be secure, that is because they are men who know not. [Qur'an 9: 6]
So thats the basics and shows that the killing of innocents isn't allowed. Yet at the same time - Islam isn't a religion which means peace in of itself, it's a religion which leads to peace - yes. But Islaam means submission. And it's a religion of justice - so if some nation comes and invades ones country - they have the right to defend themselves without exceeding the limits.
Fight in the cause of Allah those who fight you, but do not transgress limits; for Allah loveth not transgressors.
[Qur'an 2: 190]
These are basic human rights which all humane people recognise and accept.
If someone argues that Islam spreads itself to other nations by force politically, this is a satisfactory response by a Christian author;
In this formulation the claim was that jihad was better than secular conquest. Unlike Alexander the Great, Mohammed incorporated people in a polity in which they had the option of being saved, in which they had the ability to see for themselves, in which they could choose to become true believers. But it left inner conviction as something over which the individual had full control.
This argument ought to be easy for modern people to understand, or at least Americans, for they also tend to think that war can be legitimated by a high moral purpose - as long as that purpose hasn’t got anything to do with individual faith. The moral purposes they have in mind are wholly secular, not the lower level of religion, and the salvation they talk about is in this world. But they too tend to be eager to rescue other people by enabling them to become more like themselves: richer, freer, more democratic.
What do you do when your fingers are itching to intervene, when you have the power to do it, when you are sure you are right and you are convinced that the victims will be grateful - quite apart from all the advantages that may redound to yourself from intervening? Aren’t you allowed to use force? Indeed, aren’t you obliged to use it? Is it right to save people against their will? Should you force them to be free? If you say yes to these questions, you are in effect a believer in jihad.
“Jihad”: idea and history - Patricia Crone
Useful Links;
http://www.load-islam.com/artical_de...Misconceptions
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.....brave!!...LOL.... 
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