There are many non-muslim populations in similar or worse positions than any Muslim population, who don't produce religiously motivated terrorists in anything even remotely resembling the proportion of the latter population. It is orthodox Islamic (i.e. Islamist) beliefs (reference my previous post as to how this dynamic works) which are the decisive factor.
Most of those other groups have ultranationalist movements that adopt similar strategies without a religious context, as the ethnic or national group takes precedence (think Tamil Tigers, or the Uighyiur groups in Xinjiang Province, China). Arab terrorism/extremism expresses itself through religion not so much because of the religion itself, but because the various Arab "nation-states" don't correspond with any nation whatsoever. Rather than compare it even to the Balkan situation, where the sides were Bosnian Serbs (who happened to be Christian) and Bosniaks (who happened to be Muslim) and it was more of an inter-ethnic conflict than religious conflict, let's take the unique status of Iraq's demographic differences into account.
Iraq as a nation was established in 1932, as a means of a local tribal warlord (King Faisal) wresting some power over Mesopotamia away from the British Empire. This was tolerated, as it was seen as too expensive to administrate for too little resources (oil was still to come, and the British invaded in 1941 because of it). The borders were drawn up by the British Empire not because they represented any ethnic or language divisions; it was simply the easiest area for them to administer.
Flash forward to today, where Iraq has three main demographic groups - Iraqi Sunni Arabs, Iraqi Shi'a Arabs, and Kurds. Excluding the Kurds, who are much easier to understand in the post-industrialization nationalism context, the other two groups are ethnically identical. Yet, they still fight with each other - because of tribalism. Every in group needs an out group to feel superior to.
Let's expand our scope over the rest of the Arab (not Muslim) world. All of these people have arbitrary national borders set up between them. They have no clue what makes them different than their neighbor 5 kilometers away, other than there's a line drawn up by some European that says they're different, even as they speak the same language (Egypt being a very big exception to this, much in the same way Iran is, and for the same reasons - long cultural history outside of Islam). At the same time, the vast majority of these people are Sunni Muslims. The main message of Sunni Islam is the unity and brotherhood of all Muslims worldwide under the submission of one's will to God, represented most fully by the mass gatherings and meetings that occur during the annual Hajj. So even though you have all these barriers that are understandable to us from a Western perspective, it's less so from their perspective.
So where does all the violence come from? Well, a couple of things - first, petroleum, and how badly we need it. Second is the sheer brutality of Western intervention when it does occur. For example, in Iraq, we've killed around ten Iraqis, including civilians, for every Coalition troop killed in the conflict, and this is when we've been particularly careful to minimize collateral damage. Meanwhile, over the last fifty years, Western incursions and operations (such as arranging the Iran-Iraq war) have resulted in the deaths of millions of Muslims all across the world.
There had been several responses to this. First, in the more national states (Egypt and Iran), the movement had traditionally been away from foreign involvement. Khomenei definitely got many ideas from Nasser. Even Iran's stance against Israel is not so much religious (though it may be cloaked in that language) as much as it is against what they see as an incursion of Western power - keeping Israel somewhat destabilized leads to lesser hegemony over the region (since they have nukes). Second was economic warfare - expressed through the '70s oil crises. Even this couldn't hold, as the threat of Soviet incursion in the area and potential nuclear war over petroleum rose (and face it, oil is the thing that we absolutely would start lobbing nukes over) and the OPEC nations began to crack under natural economic pressures.
Thus, you have this massive group that's completely subaltern to the Western/Eastern hegemons, and very little means of recourse. After the fall of the Soviet Union, there was only one hegemonic state left, and it had more power than any since the decline of the British Empire. When the Gulf War began (which many in the area saw as a regional conflict) and the West let it be known that things would still be going by their rules, going so far as to establish military bases in Saudi Arabia, a breaking point was reached.
There's an interesting dynamic between hegemonic and subaltern actors in these sorts of relationships. The hegemon does whatever it wills, as its might makes right, and it enjoys the fruits of superiority in the relationship. It needs not to question whether it is better than the other group (tribal impulse); the situation confirms it consistently. However, the subaltern still has the tribal impulse, and a need to feel better than the hegemon which dominates most areas of the relationship. The way this usually manifests itself is in the quality of moral superiority. For example, the Southern US has been in a subaltern position with the rest of the United States since the Civil War. It is no coincidence that this is where the most emphasis on morality in the country comes from. Likewise, the heartland is subaltern to the hegemonic coastal cities, and considers those urban values to be decadent and depraved.
Flash over to the Middle East. You've had Western (and Eastern) powers interfering in your affairs for decades. They've killed millions in Muslim countries. All legitimate attempts to assert a more powerful position in the relationship have been complete failures. You have no reason to believe they'll leave you alone as long as you have more oil than they do (since 1972, btw, Africa is going to be our next major area of interest as rare earth metals, vital for computing, begin to dry up). What is this subaltern state going to do to cling to any sense of morality?
Religion, of course. Islam is taken up as the true sign of the superiority of the Muslim peoples over the decadent Christian and Jewish nations of the world, though God challenges them through the constant losing struggles they go through. God is all-merciful, as they say, and we cannot understand his will, only submit to it. Insh'allah, this situation will change one day, in their perspective. Meanwhile, since Islam has this core emphasis of all Muslims being brothers, every time a Muslim is killed in some operation performed by the Western powers, it is as if a member of their own family is killed. Soon enough, in Iraq, it is their own family members being killed, and in Arab (not Muslim, though it is important) culture, there is nothing more important than defending one's family members (which perversely explains honor killings, as the victim is being "defended" from defilement by sending her to God's judgment, as his mercy will overlook the offense given the family's submission to his will... that's religion for you).
This rage and pain grows and builds, and meanwhile you don't have any job prospects though you're intelligent and have a degree (due to being in the wrong social circles). You also hardly have any sexual prospects, either, due to the complex courtship system of the society, a distinct lack of marriageable cousins, or any other number of factors (you could be gay, too). You're not going to break this because Islam is often the only point of pride you have on the grand scale. You're broke, depressed and agitated, and nothing is going your way, either on a societal scale or a personal one.
Then someone comes up to you. Tells you that all your problems could be solved if you submit to God's will. You're confused, because you've been doing that your whole life, but intrigued. He invites you to a reading of the Qur'an. You've never heard anything like this before - the man relays the wisdom of the Prophet and the words of God to you like you've never heard before. Suddenly, you understand what he means by truly submitting to God's will. The parts that seemed contradictory before make complete sense as the man's commentary elucidates these passages for you. Your material desires seem to mean less and less as you're drawn further into a strict interpretation of Wahhabi Islam, and you begin to feel righteous and upbeat as you follow the strict interpretations.
Then your imam walks in one day, torn somewhere between anguish and rage. Everyone notices the change in demeanor, but no one knows why. He calls you and a few other of the more intelligent students into a back room to chat. Tells you of the bombing of a wedding in Pakistan. You're outraged, but feel strangely powerless, as this happened thousands of kilometers away. You speak with the imam, ask him what can be done to make the Americans account for the slaying of your brother. He tells you to meet at a location late at night, where you'll receive further instructions.
Thus, a terrorist is born. Doesn't seem so irrational spelled out like that, does it?
(sorry for the novel)