I don't quite see how he has replicated other social prejudices. I also cannot see how it follows that Dawkins and other atheists are in anyway like religious extremists. I haven't read any atheist writings that condemn and call for violence against people of faith.I don't think calling for violence is the only way to instill hate and prejudice in others. What if he were to say that being gay is against nature and those who believe it is not are irrational and unless they are challenged and choose to change their beliefs, the very fabric of our society is at risk. That doesn't wish death on anyone, but it is still hateful and damaging. Indeed, it is one of the beliefs that Dawkins identifies as harmful, and challenges.
I find his attitude to religion to be equivalent. If you single out one religion he talks about - Islam - the things he says truly are designed to polarise and to pit people against one another. He claims to want to wipe religion from the face of the earth. No, he doesn't resort to using the language of violence but that doesn't make it acceptable in my mind.
Moderate religious people compartmentalise their thinking - accepting science in one regard but reserving a special place for their faith. I think you are probably right insofar as Dawkins' takes his fight to the fundamentalists because moderates don't offer the 'culture war' that you could argue the new atheists are looking for. However, I also thinks moderates are overlooked by the new atheists because they have effectively marginalised themselves. If you are moderate enough to believe that faith is personal, that science offers a method for progressing human understanding and as such, religion has less of a place in society in terms of say making legislation then you are left with a group of the faithful that is essentially toothless.
It's interesting, though, that as I said above Dawkins flip-flops between wanting religion to have less influence and wanting to get rid of it altogether. And I also don't agree that most moderates are 'toothless'. They will certainly not be if Dawkins gets his way and faith is driven out of society. He would push people to have to fight for their right to a personal faith. Something that is protected by (amongst other things) the Universal Declaration of Human Rights. Just as he insists that all religion, taken to its natural conclusion, leads to 'young men with bombs in rucksacks', it strikes me that if his brand of atheism was taken to a logical conclusion (and if it becomes de rigeur in politics) would drive faith underground or make everyone fight. That in turn would make it look as though he was right, it would become a vicious cycle that could even create further extremism.
The crux of the 'new atheist' argument is that as a basis for understanding the universe, science offers a method based on logic and reason. As you rightly recognise, science cannot falsify the existence of a God. However, from this empirical worldview there is also no reason to invoke a higher power to explain any natural phenomenon. The bottom line is, whatever one might argue, science is irreconcilable with religion because in order to accept the tenements of any faith, one must put aside what is known about the laws of physics, biology and the universe and one must ignore the illogic that arises as a result of invoking a creator to explain its existence. Please understand that I am not attacking religious people here, I simply think that you have to accept that there has to be some suspension of reason in order to have faith.But just as there is always an element of "who created the creator" inherent in religious philosophy, there will always be unanswered questions in science. What caused the big bang (and what if the LHC doesn't find out)? There is no reason to invoke God to fill the gaps, I agree. But Dawkins only ever challenges this 'God of the gaps' theology, and it is not the only thing that draws people into faith. I don't want to believe in a god who is diminished by science, or can only exist where science can't answer our questions. I am happy for there to be things I don't understand. Sometimes faith comes from a place that just can't be explained itself. Pascal (an agnostic) used to talk about there being a 'God-shaped hole' in all of us. There is a human instinct to faith, and maybe it does involve a suspension of purely scientific thinking, but until a couple of years ago it required a suspension of scientific fact to observe a bee flying!
It involves a suspension of science and rationality to enter into a monogamous relationship, to use birth control and have sex for pleasure. Love cannot be empirically measured, laughter can't be adequately distilled into chemical processes. We don't understand the human mind; science can see chemical changes occur in the brain of someone with persistent neuroses or psychoses, so why is it not enough to correct those chemical changes to restore a person to how they were without those neuroses?
We suspend reason in order to live to the fullest. Religion is not the root of all evil, science is not the cure. Religion can be used, shamefully, as a whip to drive people to do all sorts of things. But it's humanity that does that. Yes, there are arguments and turns of phrase that are emotive and are consistently used to draw people into extremist views, but politics can do that as well. Political Islam draws heavily on communist political philosophy (read The Islamist by Ed Husain to explain this more fully), and some parts of Christianity frequently embrace politically motivated 'scientific' studies to support their views on alternative sexualities.
We are flawed human beings. I can't explain through my faith why we aren't perfect, and neither can a scientist. We came to be this way through millennia of biological, social and psychological evolution. In so many ways, we suspend reason just by being.
This debate could keep going forever, there have been arguments against creationism for as long as there has been a capacity for human thought, so I'll leave it there.