They do not advocate the indiscriminate murder of people perceived to be in opposition to their beliefs. They do not want to take over the world and implement a 7th century legal system that is extremely violent and (look at Saudi Arabia) easily used as a barbaric tool of oppression. These are huge distinctions, you must realise that. Dawkins et al bear little resemblance to extremist clerics. They also have evidence and reason on their side. Islamist's have an ancient text anchored on a supernatural supreme being that carries no weight of convincing evidence for it being the authentic word of that being. I mean, if it did, everyone would be a Muslim. That is your acid test right there.
I agree that the West played a major part in the mess. But I am not convinced from what I have learnt about Islamic history, moreover the complete lack of consensus on what Islam actually is and how it is to be interpreted that ISIS are not real Muslims, because Islam is so open to interpretation. The Islamic state espouse a clear religious motive that details their new path for Islam right up to the day of judgement and the end of the world.
I would refute any accusations of being Islamaphobic. I find all the Abrahamic religious texts to be damaging and fundamentally divisive. Just look at Israel, the place is completely insane. I went to church as a child and was forced to Sunday school also but I am now an atheist. It is the only logical position for me. I find the notion of an afterlife inconceivable and the Islamic description of it seems especially ridiculous. That does not mean that I am not respectful of Muslims in everyday life. Muslims are people just like anyone else and are good for a laugh and conversation. The Muslim posters on here all seem like good guys. I do feel that we should be able to freely debate and criticise, in a constructive way, the teachings of Islam, the history of Islam and the content of the Islamic text freely, however.