One of the biggest misconceptions people seem to have about Islam is surah 9:5 which is often translated as:
When the forbiddden (sacred) months are over, then fight and slay the unbelievers where you find them, and lie in wait for them in every stratagem of war...''
Firstly, something that strikes me is that nearly everyone who cites this as evidence of Islam's intolerance DOESN'T seem to quote this passage in its entirety. This is the rest of the passage:
''...but if they repent and establish regular prayers and give in charity, then open the way for them, for Allah is Most Gracious Most Merciful''
But to get to the point, this particular passage, to my understanding at least, was aimed at a specific set of unbelievers. Looking at the Arabic root word 'translated 'unbelievers', the root being sh-r-k, which gives you words like 'shirk' (basically, polytheism or worship of others besides Allah). The construction 'mushrikiin' is indicative of a person or people doing some action, and so a better translation would be 'polytheists'. Now my understanding of this passage is that it was revealed at a time to deal with a specific set of unbelievers, likely the pagan Quraysh who worshipped hundreds of idols, or other pagan forces fighting against the Muslims in Medinah. I don't have a tafsir (commentary) or other ways to be certain about this.
The Qur'an is also clear that where a peaceable solution between Muslims and other peoples is possible it should happen, such as the Constitution made in Medinah just after the hijrah, which saw Muslims, the Medinah Jewish groups and friendly pagan groups accorded the same rights and responsibilities as each other. In Muslim Moorish Spain, Muslims, Jews and Christians lived peaceably for the most part, even attending the same schools and sharing places of worship as well as having the same legal recognitions. The Qur'an actually teaches that good Christians and Jews will be rewarded by Allah and there is no single verse which preaches either forced conversion or oppression.
With regard to the second part of the passage I quote, there is much room in Islam for sincere repentance to Allah, and where a person wishes to do so, they should not be prevented from doing so. Even those who have committed the greatest of sins can be forgiven if they cease their wrongdoing, admit their wrongdoing to Allah and then aim to avoid that sin again.