First of all I'm not a fan of this term "New Atheism". To me it just reeks of propaganda and often used as a pejorative for Atheists who have anti theistic opinions especially by the likes of Glenn Greenwald, Reza Aslan and well known Twitter jester CJ Werleman. Kyle Kulinski once said "New Atheists are Atheists who are finally speaking out". There is nothing "new" about anti theism and this absurd hysteria that surrounds the "New Atheists"often makes people forget anti theistic critiques of religion preceding them from the likes of Bertrand Russell, Karl Marx, Thomas Paine, Ludwig Feuerbach and Lucretius.
Karim's argument is that the "New Atheists" are soft on Israel and "avoid to hold Israel unaccountable" for its brutality. He bases his argument entirely on things Sam Harris has said on Israel and completely ignores the other "New Atheist" figures. Karim and other critics of "New Atheists" seem to be committing the same fallacy that they accuse "New Atheists" of committing in relation to muslims which is the hasty generalisation where one generalises an entire group of people based on the actions or words of a few. So he might aswell have titled his article "Sam Harris and Israel".
In fact there is divergence of opinions on political issues amongst "New Atheists" for example on the issue of Israel-Palestine Hitchens was a committed anti-Zionist and derided people like Daniel Pipes for minimising the suffering of the Palestinians. Richard Dawkins last summer tweeted about how the destruction of Gaza was "obscene" and he also expressed bemusement at "why should Palestinian Arabs be the ones who pay for the crimes of Hitler" when talking of the establishment of The Jewish State in 1948. PZ Myers who is often called a "New Atheist" wrote a blog post where he called for the USA to "end support for Israel" and attacked Sam Harris for his views on Israel so there are "New Atheists" that acknowledge Israeli brutalisation towards Palestinians.
Of course there are other outspoken Atheists that are more sympathetic to Israel such as Bill Maher and Ayaan Hirsi Ali. All I'm saying is the people associated with "New Atheism" do not have a monolithic opinion on Israel and it is quite unfair to generalise their opinions on the conflict based on what Sam Harris said in his podcast.
As far as Karim's general criticisms are concerned I actually don't disagree with all of it. I agree with him when he criticises Sam Harris for minimising the suffering and hardship of the Palestinians which included the expulsion of thousands of Palestinians in 1948 -popularly known as Nakba which is very important in the Palestinian story- that led to the creation of the refugee crisis. We now have a situation where 4th generation of Palestinians either live in exile, squalid refugee camps, dispossession or under occupation and humuliation. This isn't something that can be glibly dismissed especially as there are elements within the Israeli far right who would want to and have openly said they would have rid of the Palestinians.
I also think he makes a good point when he says that it is a mistake to see the conflict cause as purely a religious one. The conflict is a battle of two secular nationalisms that represent two small peoples of equal size and have equal stake in the land fighting over territory, identity, culture, history and injustice though it took until the 1970s for the world to see this as the true representation of the conflict. This is not to say religion played no part as both the Zionist movement and the Palestinian movement used religious imagery and mythology to justify their claims to the land but they were not theocratic movements.
The Palestinian national movement is not a monolithic movement as you have groups like Fatah which is in principle a secular and social democratic party and PFLP which was a Marxist group founded by a Christian named George Habash alongside Islamist groups like Hamas and Islamic Jihad.
However ever since the 1967 war religion has had a bigger influence on the conflict from both sides. On the Jewish side Religious Zionism became more popular which eventually led to the rise of religious based and right leaning groups like Jewish Home, Likud, Shas and to the more extreme end National Union, The Kahanists and the ideological settlers on the West Bank.
The hard line and messanic elements of this movement hold on to Eretz Yisrael which the idea that God gave The Land of Israel exclusively to the Jewish People and therefore in order to achieve this more land has to be gobbled up through settlements and if possible expulsion of Palestinians then finally the Jewish people will be saved.
It's obvious that this is sheer utopianism and a barrier to peace as it gives the impression to the Palestinians that the Israelis aren't really interested in peace and only interested in stealing their land. These extremists are not only a threat to Palestinians but also a threat to Israel's increasingly fragile secular and democratic nature.
Since the 1980s Islamism became a significant part of the Palestinian movement with the rise of Hamas the Palestinian offshoot of the Muslim Brotherhood. ( in part with help from Israel to fight the PLO) In addition Islamists have co-opted the Palestinian issue as a vehicle for their blatant genocidal anti-semitism and their fantasy of reviving a caliphate that will unify the muslim world whether it is the muslim brotherhood, Hizb ut-Tahir, Hezbollah and their Iranian paymasters and the various Salafi Jihadist groups.
This does change the dynamic of the conflict because the rise of religious extremism on both sides means that the parties of God hold a veto on the peace process which makes peace harder to achieve and holy war more likely because the hysterical rhetoric breeds more hatred and suspicion of the other especially as the extremists are making absolutist and exclusive claims to the land based on the religious identity of their respective tribe.
Karim claims that Hamas has supported the two state solution since 2006 based on the "repeated statements of its leaders" he does not give any evidence for this. I have to say it seems ironic for Karim to lambast Sam Harris for blindly believing what the Israeli government says but why should we believe anything Hamas says either? It's all well and good for them to write letters to The Guardian and other Western media outlets saying "they have no quarrels with Jews only with Israel's policy". It's quite funny as Salafist Jihadis deride Hamas for their "moderate" stance vis-a-vis Israel.
On the other hand when Hamas speaks to Arab audiences then this "moderate" tone wears off. They essentially repeat the same violent fanatical rhetoric for instance in 2012 Ahmad Bahr, Deputy Speaker of the Hamas Parliament, stated in a sermon that the Jews should be annihilated. This combined with the fact Hamas has not altered its charter to demonstrate its change of view and its deliberate taregetting of civilians with its rockets shows we should be very skeptical whenever Hamas is in one it's "moderate" phases.
In summary for all the good and interesting points Karim brings up I frankly think it is absurd to claim "New Atheists" (already a bad and very vague term) have some kind of "marriage" with Israel and by Israel Karim means the Israeli right. Especially as he bases his entire argument on things Sam Harris only one member of the "New Atheists" has said and ignoring the diverging and nuanced opinions of other "New Atheists" like PZ Myers, Christopher Hitchens and Richard Dawkins. Karim seems like a reasonable person and I hope he soaks in some of my criticisms which hopefully will make him think through his position.