I completely agree with Mr.Artha and appreciate for understanding how
Qur'anic verses are misused to prove that Islam is an intolerant and aggressive religion. I can reply to the verses that Minerva has quoted and I can see the verses have been quoted out of context .

Just as there is a verse in the Qur'an where it says "whereever you see a polytheist ,kill him". Offcourse if we just read this verse it means that we are ordered by Allah to kill any polytheist that we see around us but if one reads such verse in its proper context, then we understand the main implication of such verse.

Such verses were revealed for perticular time and circumstances that cannot be generalized. There was actually a battle between polytheists(pagans) of Makkah and the muslims and because of there strong oppression and persecution of muslims, God revealed such verse so that muslims can defend themselves from such situation.

There is also a verse just before or after this verse which says that if any of the attacker or polytheist seeks asylum ,provide him asylum and not only that but also take him to a secure place.
Now I want to ask all those people who criticise Islam,that which Army General is so generous and kind hearted in this world who will forgive a person who is on the opposition side in the battle?

Dear brother/Sister.
You had asked a tricky questions..
A few selected verses from the Qur’an are often misquoted to perpetuate the myth that Islam promotes violence, and exhorts its followers to kill those outside the pale of Islam.
1. Verse from Surah Taubah

The following verse from Surah Taubah is very often quoted by critics of Islam, to show that Islam promotes violence, bloodshed and brutality:

"Kill the mushriqeen (pagans, polytheists, kuffar) where ever you find them."
[Al-Qur’an 9:5]
2. Context of verse is during battlefield

Critics of Islam actually quote this verse out of context. In order to understand the context, we need to read from verse 1 of this surah. It says that there was a peace treaty between the Muslims and the Mushriqs (pagans) of Makkah. This treaty was violated by the Mushriqs of Makkah. A period of four months was given to the Mushriqs of Makkah to make amends. Otherwise war would be declared against them. Verse 5 of Surah Taubah says:

"But when the forbidden months are past, then fight and slay the Pagans wherever ye find them, and 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."
[Al-Qur’an 9:5]

This verse is quoted during a battle.
3. Example of war between America and Vietnam

We know that America was once at war with Vietnam. Suppose the President of America or the General of the American Army told the American soldiers during the war: "Wherever you find the Vietnamese, kill them". Today if I say that the American President said, "Wherever you find Vietnamese, kill them" without giving the context, I will make him sound like a butcher. But if I quote him in context, that he said it during a war, it will sound very logical, as he was trying to boost the morale of the American soldiers during the war.

4. Verse 9:5 quoted to boost morale of Muslims during battle

Similarly in Surah Taubah chapter 9 verse 5 the Qur’an says, "Kill the Mushriqs where ever you find them", during a battle to boost the morale of the Muslim soldiers. What the Qur’an is telling Muslim soldiers is, don’t be afraid during battle; wherever you find the enemies kill them.
5. Shourie jumps from verse 5 to verse 7

Arun Shourie is one of the staunchest critics of Islam in India. He quotes the same verse, Surah Taubah chapter 9 verse 5 in his book ‘The World of Fatwahs’, on page 572. After quoting verse 5 he jumps to verse 7 of Surah Taubah. Any sensible person will realise that he has skipped verse 6.
6. Surah Taubah chapter 9 verse 6 gives the answer

Surah Taubah chapter 9 verse 6 gives the answer to the allegation that Islam promotes violence, brutality and bloodshed. It says:

"If one amongst the pagans ask thee for asylum,grant it to him, so that he may hear the word of Allah; and then escort him to where he can be secure that is because they are men without knowledge."
[Al-Qur’an 9:6]

The Qur’an not only says that a Mushriq seeking asylum during the battle should be granted refuge, but also that he should be escorted to a secure place. In the present international scenario, even a kind, peace-loving army General, during a battle, may let the enemy soldiers go free, if they want peace. But which army General will ever tell his soldiers, that if the enemy soldiers want peace during a battle, don’t just let them go free, but also escort them to a place of security?

This is exactly what Allah (swt) says in the Glorious Qur’an to promote peace in the world.