From Qur'an, Allaah says (translation of the meaning):
Whosoever kills a human being for other than manslaughter or corruption in the earth, it shall be as if he had killed all mankind, and whoso saves the life of one, it shall be as if he had saved the life of all mankind...
[Qur'an Ma'idah 5: 32]
Allah forbids you not, with regard to those who fight you not for (your) Faith nor drive you out of your homes, from dealing kindly and justly with them: for Allah loveth those who are just.
Allah only forbids you, with regard to those who fight you for (your) Faith, and drive you out of your homes, and support (others) in driving you out, from turning to them (for friendship and protection). It is such as turn to them (in these circumstances), that do wrong.
[Qur'an Mumtahinah 60: 8-9]
The Messenger of Allaah (peace be upon him) said [translation of meaning]:
“Do not kill any old person, any child, or any woman.” [Abu Dawud]
“Do not kill the monks in monasteries,” or “Do not kill the people who are sitting in places of worship.” [Musnad Ahmad]
Narrated Anas ibn Malik: The Prophet (peace be upon him) said: Go in Allah's name, trusting in Allah, and adhering to the religion of Allah's Apostle. Do not kill a decrepit old man, or a young infant, or a child, or a woman; do not be dishonest about booty, but collect your spoils, do right and act well, for Allah loves those who do well. (Sunan Abu Dawud , Book 14, Number 2608)
It is narrated by Ibn 'Umar that a woman was found killed in one of these battles; so the Messenger of Allah (may peace be upon him) forbade the killing of women and children.
[Sahih Muslim, Book 019, Number 4320]
All the above is in the context of fighting. Outside of the war-zone none of that is permissible - unless there is a certain law which calls for capital punishment by a just judge. [Refer to Capital Punishment.]
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.But in context it is referring to those who are in a state of warfare with the Muslims.
[Qur'an Al-Tawbah Repentance 9:5]
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).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.These are basic human rights which all humane people recognise and accept.
[Qur'an 2: 190]
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