This is a simplistic, incorrect interpretation of the motivations of the 9/11 attackers. They did not wake up one morning and say God or the Quran said to fly a plane into a building. They rationalised it as an act of revenge for America attacking them first. Bin Laden's language has religious terminology but the reasoning is no different to America stating they bombed Hiroshima because Japan attacked them first or Putin saying he is attacking Ukraine because he thinks his land, Russia, is under attack from NATO. These motivations would remain whether they were Muslim or atheist.
I'm not suggesting that they just had an instantaneous religious conversion, and I agree that it's against a convoluted backdrop, but the explicit claims of the group responsible were that it was a religious activity. And that's not unique to Islam, that's exactly the same as the explicitly religious motivations for at least some of the Crusaders during the Middle Ages, to pull a Christian example.
Whether the claim that it was partially, largely or entirely a religious expression is important in the broader sense, but for the purposes of what it did to the Western (and American in particular) perception of religion when it was depicted as such it doesn't really matter very much.
Western soldiers are called to bomb people in other countries as part of their patriotic duty or because it is in their country's national interests or because they are told that their country or way of life is under threat, so being religious didn't cause 9/11.
Religion, in part, along with racism and nationalism, fomented the geopolitics that led to all the precursors: Soviets and then the West in Afghanistan; the West in Kuwait to oppose Iraq; the West's interference in Iran; even back to the debacle of handing Palestine over to the new Jewish State after the 2nd world war. Religion was a part, at least, of the response that included 9/11, and it doesn't matter if it was a large or small part, because it brought to the attention of the West that religion was not necessarily the inconsequential social club that it had become to them, it could still be visceral and profoundly motivating - for good or ill.
It was in the wake of that realisation that the 'New Atheist' movement gained traction.
You are looking at the wrong bogeyman if you are blaming religion - you could just as easily say the problem is the existence of nation states or government or private ownership of land or money or resources or political parties or foreign policy.
For me, personally, I think that Islam was a contributory factor; in particular, the (I think it's Wahabist?) particular 'hard-line' Islam that is espoused by Isis and the Taliban which takes such an absolute and authoritarian stance that's so at odds with Western values. Nation states are not a necessity, in theory, there are other ways of arranging groups of people (indeed, at least some of the issues in Africa and the middle-East come from European colonial powers implement 'nation state' political boundaries into cultures that operated as overlapping tribal and cultural diaspora).
Nation States, though, are not pitched as absolute - you can revolt against the ruling class, you can changes the laws of land ownership, you can transfer ownership of money or resources in any number of ways. Religion, though - in particular the Abrahamic religions which are so deeply entrenched in all this - pitch themselves as inviolable, sacred and beyond question, even whilst they violate, desecrate and question each other. Religious claims are categorically different from the other concepts that you mention, and therefore pose different problems and threats.
O.
