Most of the critics of Islam quote the verse kill the Mushrikoon (polytheists) where ever you find them , The Holy Quran, Chapter 9, Verse 5 to show that Quran Commands the killing of Disbelievers
This is quotation taken completely out of context. If you read the chapter(Surah At-Taubah) from the beginning the first verse talks about the treaty between the Muslims and the Mushriks (Pagans) of Mecca who used to persecute the muslims who as of yet had not retaliated.
Freedom from obligation (is proclaimed) from Allah and His messenger toward those of the idolaters with whom ye made a treaty , The Holy Quran, Chapter 9, Verse 1
In the next verse The Meccans are given four months time to set things right otherwise a declaration of War and coming to verse [9:5], the complete verse is
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 practice regular charity, then open the way for them: for Allah is oft-forgiving, Most merciful." The Holy Quran, Chapter 9, Verse 5
Hence if you read this in context we know that this statement was made in the battle field. Critics often fail to quote with context. Infact in the battle the Quran Commands that a person who seeks asylum should be escorted to a place of security.
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." The Holy Quran, Chapter 9, Verse 6
The Quran explicitly forbids killing. Whosoever kills a human being for other than Murder or Creating Mischief in the Land, it is as if he had killed the whole of Human Kind and whoso saved the life of one as if he has saved the life of all Mankind The Holy Qur'an, Chapter 5, Verse 12
People must appreciate that the Quran contains instructions and details of incidents that occured in the past. In this case the historical background is relevant, as the reason for revelation was to enable the Muslims to defend themselves from the constant persecution from the meccans. This is not a general principle as anti islamists see it, which commands all muslims to kill disbelievers.
Regarding your second quote its from surah 9, which again has to be looked at in its full context. I will give it below then you tell me if what is being said is in anyway unfair or promoting terrorism. I'll start from verse 6 so you can see the full context. (I will put the context in the brackets below if you cant understand the verses)
6. 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.
(Muslims are ordered to protect the disbelievers and not only that but to take them to a place of safety)
7. How can there be a covenant with Allâh and with His Messenger for the Mushrikûn (polytheists, idolaters, pagans, disbelievers in the Oneness of Allâh) except those with whom you made a covenant near Al-Masjid-al-Harâm (at Makkah)? So long, as they are true to you, stand you true to them. Verily, Allâh loves Al-Muttaqûn (the pious - see V.2:2).
(If people are honest then respect the honesty and remain truthful with the non believers - God loves the truthful)
8. How (can there be such a covenant with them) that when you are overpowered by them, they regard not the ties, either of kinship or of covenant with you? With (good words from) their mouths they please you, but their hearts are averse to you, and most of them are Fâsiqûn (rebellious, disobedient to Allâh).
(God is telling the Muslims to beware of the dishonest unbelievers and to avoid making agreements with them as they may breach)
9. They have purchased with the Ayât (proofs, evidences, verses, lessons, signs, revelations, etc.) of Allâh a little gain, and they hindered men from His Way; evil indeed is that which they used to do.
(The people have distorted the truth and promote evil)
10. With regard to a believer, they respect not the ties, either of kinship or of covenant! It is they who are the transgressors.
(The dishonest dont respect their family ties or friendship let alone a covenant with the believers)
11. But if they repent, perform As-Salât (Iqâmat-as-Salât) and give Zakât, then they are your brethren in religion. (In this way) We explain the Ayât (proofs, evidences, verses, lessons, signs, revelations, etc.) in detail for a people who know.
(Despite this if these dishonest people repent then forgive them as they are your brothers)
12. But if they violate their oaths after their covenant, and attack your religion with disapproval and criticism then fight (you) the leaders of disbelief (chiefs of Quraish - pagans of Makkah) - for surely their oaths are nothing to them - so that they may stop (evil actions).
(But if they break an agreement and ATTACK YOU FIRST they show the promises they made mean nothing)
13. Will you not fight a people who have violated their oaths (pagans of Makkah) and intended to expel the Messenger, while they did attack you first? Do you fear them? Allâh has more right that you should fear Him, if you are believers.
(Should you not defend yourself against people who commi such actions, those who break agreements and make war on you?)
14. Fight against them so that Allâh will punish them by your hands and disgrace them and give you victory over them and heal the breasts of a believing people,
(You should fight such people and restore order and punish the traitors for their actions)
So as you can see, its not just a matter of killing disbelievers. The Quran tells us to protect them, but to fight back if attacked first. This is not terrorism, and to quote this verse out of context is unfair.