Thanks to globalisation, they have much stronger links with the wider Muslim world - and share Muslim anger over such issues as Palestine and Iraq.
Bloodshed at the mosque
But much less clear is who is behind the recent violence.
Take the events of a single day, 28 April last year.
I visited the ancient and revered Kru Se mosque in the town of Pattani, where 32 Muslim militants were killed by the Thai security forces after a nine-hour standoff.
But the drama at the mosque was only the climax of a day of violence which claimed over 100 Muslim lives.
It was the bloodiest day of fighting since violence resurfaced in the region in January
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In a series of apparently co-ordinated incidents, Muslims attacked police posts across the three southern provinces.
Given that they were armed only with knives and machetes, these were virtually suicide missions.
But who these militants are, and what drives them, remains a mystery.
I asked Nur, whose husband Mohammed was one of those who died on 28 April, why she thought he had done it.
He just went off one day, she said, and didn't return. Even now, she has never seen the body.
Experts can shed some light on the puzzle, but not much.
They believe an older separatist movement - active in the south in the 1960s and seventies - has now been superseded by a newer Islamic one.
Government advisers in Bangkok go further and allege the involvement of Jemaah Islamiyah, regarded as the regional arm of Al-Qaeda.
But they offer little by way of proof.
Fish and fertilisers
"The people love the army," I was assured by the military spokesman in the south, a smooth-talking man known as Colonel Sam.
In an effort to convince me, he took me to see smiling villagers who'd received fish and fertilisers, as well as protection, from Colonel Sam and his soldiers.
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The reality is that the Muslims of the south deeply resent the Thai army and its pervasive presence
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But virtually all of them were Buddhists - the Muslims, I was told, were praying at the mosque.
In one village Thai flags had been placed every few metres along the roadside.
Colonel Sam gave the villagers a pep talk, urging them to show the BBC how strong and united they were.
It all felt rather staged.
A wider insurgency?
The reality is that the Muslims of the south deeply resent the Thai army and its pervasive presence.
Thanks to the events at Tak Bai, the militants now seem to enjoy more grass-roots support than before.
In national elections on 6 February, Prime Minister Thaksin Shinawatra won a landslide victory and four more years in power.
Most experts think he has mishandled the conflict in the south.
The danger is that, if his government sticks with its hard-line strategy in the south, the insurgency will be transformed from a local problem into a regional or even an international one.