I'm a nonbeliever, but I don't have much love for the New Atheism crowd. However, a number of my friends have bought into them big time and they all too often make claims like the one above. What counter arguments are there to such claims?
If they claim that this is the case for all wars, all you have to do is give one counter-example, such as the 1990 Gulf War, or the Second World War, or the First World War, or the 1870 Franco-Prussian War, or the Napoleonic Wars, or the War of the Austrian Succession, or the War of the Spanish Succession - I think you get my point. ^(With apologies for my euro-centrism.)
If their claim is that most or many wars are caused be religion, that would be harder to argue against, because that is such a vague statement. Such a statement can only be proven or disproven by making a comprehensive study of the causes of all wars. And if you are able to find clear causes for a war, you'll see that seldom there is one single cause for a war.
For instance in my own area of expertise, the "Dutch Revolt" was partly religiously inspired, but there were political and economic grievances as well. In fact, the "Dutch Revolt" is best seen as a series of revolts, only one of which was sparked by religious persecution. That one didn't lead to the full scale revolt though. It was the imposition of taxation and the bypassing of political assemblies which sparked the revolt which led to all-out war.
All in all, I think for most wars it is too simplistic to say "X caused the war", and thus a statement like "X causes the most wars" is nonsensical.
Turn and walk away. You could present any number of counter-examples and the next talking point is to find one person on either side of the conflict who says "God is on our side" and hey, instant religious war.
With examples: here's a non-comprehensive, reverse chronological list of major conflicts in the last two centuries that quite simply were not 'caused by religion':
Religion has caused many wars, and it has been a factor in many more; religious dimensions can be powerful accelerants for secular conflict, and they are often used by belligerents to do exactly that. But in all of the conflicts I listed above, the primary drivers were political, economic and social issues, not spiritual ones.
The 'all wars are caused by religion' trope tends to rest on three legs:
Even some of the most 'obvious' examples of the 'religion causes wars' paradigm start to fall apart upon closer examination. The best example I can think of would be The Troubles in Northern Ireland. Yes, there's a strong sectarian dimension to that conflict — but at its root, it's fundamentally a political-territorial conflict, not a religious war. (I recently wrote a long answer to a question about the Troubles which touches on this topic.)
In my experience, as soon as you start deconstructing the causes of conflict, the idea that there's any single capital-c Cause — and particularly the idea that religion is that cause, in most cases — falls quickly by the wayside.
I'm hesitant about the way you put the question. When it comes to history, you shouldn't really be looking for arguments for one thing or another to validate your beliefs. Don't get me wrong, it is at the core of it a perfectly valid question, but then you should also present it as that core. For example "Were all or most wars caused by religion?"
I'm not answering your question here, so perhaps my comment is a little bit too meta and should be removed. If so I'm sure a moderator will oblige.
The wars that caused most casualties and which were all fought in the 20th century, were all non-religious affairs. Whether it is WW1, WW2, the Russian or the Chinese Civil Wars or the wars in Korea, Indochina and Congo. Millions died and non of these conflicts were caused or inspired by religion.
In general, as Clausewitz states, wars have three main characteristics: A political element which sets the goals in a war, a military element that represents the skills, genius and methods to fight a war and there is the people that provides "fuel" for the war in the form of hatred and popular commitment.
Religion can be an important part of the third characteristic. Politicians and generals have used religion to their advantage in order to gain popular support, new soldiers and societal cohesion. But in the 20th century religion wasn't the driving factor for the most deadly conflicts ever. In other times that might be different, but there are always more arguments and circumstances that create a situation called "war" than only religion.
I will be happy to be corrected if I am wrong. I understand that most wars fought to date tend to be over resources or access to resources. No matter what window dressings you put on them to justify the war.