The point of criticizing the Courtier's Reply is that Dawkins, Harris, et. al. aren't spending a lot of time delving into the minutia of theology. They are responding to the very basic claim that a god exists; usually the response is, "I am not convinced of your claim, therefore I will not pretend that it is true." Rebutting this basic claim requires no theological background; if there was evidence that a divine entity existed and that it created the universe, religious apologists would not have to resort to dishonest word games to defend their position.
Likewise, it doesn't require much theological knowledge to show that the qualities overwhelmingly ascribed to an Abrahamic deity (omnipotence, omniscience, and omnibenevolence) are incoherent and contradictory qualities and can therefore be dismissed out of hand -- like a married bachelor, it's one of those rarified abstractions that we can conclusively show does not exist.
I disagree with Harris when he starts jumping the gun and saying that Arabs should be profiled at airports, but I don't find anything wrong with his assertion that Islam is the most dangerous religion today. There is plenty of evidence outside theology that shows this to be the case.
Oops. I think I accidentally moved the goalposts a bit - away from simplified anti-religious attitudes and towards theological debate. I don't have enough knowledge about theological issues to say anything more than the way the "new atheists" usually represent theology is oversimplified. The discussion about the existence of god doesn't really interest me since I haven't yet heard a convincing argument supporting that claim and see the probability of those arguments existing being too small to bother looking for them. Religions themselves, reasons that people believe in god(s) or otherwise practice religions and the parts they represent in the puzzle that is humanity are among things that intrigue me.
Claiming that Islam certainly is the most dangerous religion is utter horseshit. There is a possibility that it somehow is but there is nothing obvious in it. Religion is something that can't be analyzed by separating it from the societies and cultures that have formed it, influence it and are formed and influenced by it. If you only look at the religion and its texts and doctrines you miss most of the picture. For example, most of the radical sects in Islam have been born in the Middle East and have spread from there to the rest of the world. To understand why this is, you have to understand the political and cultural circumstances in the societies there to see how they have formed. To understand why they have spread elsewhere you have to understand the reality and everyday life of the Muslims in different parts of the world. While most Muslims don't live in the Mid East it's a hotbed of sectarian and political conflicts that influence the Muslim community globally. Also, religious interpretations justifying things like female genital mutilation and burqas have their roots in local cultural traditions and patriarchy. These express themselves through the religion but the roots of the problems are elsewhere.
Are certain expressions of religion more fertile ground for different abuses? Yeah. Are all? No. Maybe authoritarianism and certain personality types that thrive and are comfortable in that kind of environment are the root causes and removing the religious aspect might make them look other ways to fulfill this need. In my opinion there are very few comfortably definite answers to be found here, mostly only different viewpoints, different degrees of probability and more questions.
Just one example of how a fundamental moral problem is surprisingly little influenced by religion:
global poll about justification of violence toward civilians. There are a lot of variations between different geographical areas but within any given area the influence of religiousity is statistically insignificant. Oh, and the area where people disagree most with civilians committing violence towards other civilians being justified in any circumstances? Middle East and North Africa.
