Applying the "Propoganda Model" (crafted by Herman with Noam Chomsky; see Manufacturing Consent: The Political Economy of the Mass Media) to the recent history of genocide and bloodbaths, the Herman and Peterson demonstrate how politicized the term of genocide is: reserved for our official enemies, but ignored when the US or its allies carry out the killing.
The authors briefly review major bloodbaths and genocides in the past 30 years, particularly with regard to their depiction in the mainstream Western media. Thus readers should be aware that this book does not go deeply into the events and history surrounding the bloodbath/genocide.
Another question is why Afghanistan wasn't a separate case in the book. Dasht-e-Leili, a massacre of several thousand by the Northern Alliance, is included, but not the country as a whole. Since this treatment is granted to Iraq, it is unclear why it is not similarly given for Afghanistan. Even, for example, the initial bombings in late 2001 may have resulted in as many as 20,000 casualties. 
A casualty of the cursory treatment given to each atrocity is that competing narratives of a bloodbath/genocide are not given much space. This is not a problem for most of the cases, as they are generally uncontroversial at to the facts. However, the chapter on Rwanda has received strong backlash from some academics. Herman and Peterson appear to be aware of how controversial their thesis is (which is that it was the Hutus, and not the Tutsis who suffered the majority of casualties from the genocide), and devote the most text to it than for any other atrocity.
Having read Gerald Caplan's review of Politics of Genocide and the responses that followed, I've concluded the following, speaking as a non-expert on the Rwanda genocide:
*A key piece of evidence presented by the authors is a study written by Christian Davenport and Allan Stam; they quote from the study: "[t]he killings in the zone controlled by the FAR [i.e., the Hutu-controlled Armed Forces of Rwanda] seemed to escalate as the RPF [Rwandan Patriotic Front, the main Tutsi militia] moved into the country and acquired more territory. When the RPF advanced, large-scale killings escalated. When the RPF stopped, large-scale killings largely decreased." (58) However, Herman and Peterson make no compelling case to attribute these killings to the RPF. On his blog, Adam Jones, a student of genocide, notes this "fits with a picture of Hutu Power agents lashing out genocidally at Tusis, in spasms that correlate with RPF advances."
*The authors also quote from a September 1994 State Department memo which notes that the "[RPF] and Tutsi civilian surrogates [killing] 10,000 or more Hutu civilians per month, with the [RPF] accounting for 95% of the killing." (57) However, that would lead to, in a few months time, thirty or forty thousand Hutus dying, which conforms to the 'standard model' or the genocide. To reach the level of Hutu casualties argued for by Herman and Peterson, such a rate of killing would have to continue for more than five years for Hutus to make up a majority of casualties.
The authors do bring up an important point in that no Tutsi or member of the Kagame regime has been prosecuted for war crimes. If the above memo is correct, that is indeed a travesty of justice.
*The case that "the RPF was the only well-organized killing force within Rwanda in 1994" isn't made as strongly as it should have been, considering this part of the authors' argument is so integral to their overall conclusions. The authors state that three consecutive prime ministers were "either pro-RPF or subsidized by it", a pro-RPF minister headed the civilian intelligence agency, and "Rwanda's "integrated" military then combined the armed forces of the Tutisi-lead RPF that was seeking to overthrow the government alongside the government's regular army". (129) It's unclear why the government's regular army isn't considered a 'well-organized killing force' or, for that matter, why the Interahamwe militia isn't also included in this category. For example, according to Gerald Caplan , Belgian intelligence reported "at the end of 1993 that `The interahamwe are armed to the teeth and on alert...each of them has ammunition, grenades, mines and knives. They are all waiting for the right moment to act'".
*While informing the reader that the US desired a different regime in power in Rwanda, the authors never explain why. What was Habyarimana doing that was so objectionable to the US government?
*The authors claim that Tutsi forces mobilized "60 to 120 minutes" (56) after Rwandan president Habyarimana was killed, providing evidence that the killing was preplanned by the RPF. However, the source for this is a public lecture by Allen C. Stam; I may be nitpicking here, but a better source is preferable.
*Herman and Peterson find it "incredible in the extreme" that "Rwanda would be the first case in history in which a minority population, suffering destruction at the hands of its tormentors, drove its tormentors from power and assumed control of a country". (56-57) However, I agree with Adam Jones  that Herman and Peterson are "conflating Rwanda's civilian Tutsis with "Kagame's Tutsi forces"", given that the RPF was, by Herman and Peterson's own admission, an outside invading force.
*One point not mentioned in any of the responses to Herman and Peterson is why the Hutu government's UN ambassador pleaded for more UN peacekeepers while Paul Kagame and the RPF desired the opposite. It seems that those carrying out genocide would prefer not having outside observers of any kind.
One should be able to attack conventional wisdom, whether it's physics or genocide, without being attacked personally. Unfortunately Herman and Peterson were immediately labeled genocide deniers and part of the "lunatic fringe", as Caplan put them (the authors one-upped Caplan by accusing him of being a "genocide facilitator"). Their work deserves serious attention and, if necessary, serious rebuttals.
 Steele, Jonathan. May 20, 2001. "Forgotten victims". The Guardian.
 Caplan, Gerald. June 17, 2010. "The politics of denialism: The strange case of Rwanda". Pambazuka News.
 Jones, Adam. July 15, 2010. "On genocide deniers: Challenging Herman and Peterson". Pambazuka News.