I think it's because that area has a higher concentration of Islamic radicals, and their culture is in many ways stuck in the middle ages - violent, vengeful, conservative. It's a vicious cycle because such a culture breeds more Islamic radicals, which then encourage such a culture further. The worst example of that in practice was the Taliban in Afghanistan.
Neither of the above seem like innately permanent things. But the only way to solve them, besides letting them sort themselves out, is benevolent Western imperialism (e.g. Iraq, Afghanistan, and as opposed rather more barbaric 19th and 20th century Western imperialism). Still, I doubt you'll find many champions of that route except, perhaps, the American neocons.
It's not specifically because of Islam. I mean, it (religious radicalisation) could just as easily have happened if it was Judaism that had become dominant instead, and did in the past with Christianity.
Turkey is different both culturally and historically. Besides being a different society and ethnic group to the Middle East, 100 years ago their military had the foresight to enforce the separation of church and state (and the rather poor judgement to purge Armenians). Malaysia and Indonesia, on the other hand, were never part of the Middle East, and before adopting Islam recently (relatively), already had vibrant and diverse local cultures, producing a somewhat moderating effect on fundamentalism. They also weren't conquered by Muslims, rather converted peacefully by traders.
