Jemaah Islamiyah is the primary Islamist organization in Indonesia and they are facing major difficulties today.
The old JI command structure may have been destabalized. The markaz was the JI command headquarters. It governed 4 mantiqi (regional commands), each with about 12 wakilah that governed the smaller cells and networks. JI only had a few thousand operatives at its peak, and carried out a few major terrorist attacks – like the one on Bali.
JI never became a big power. Indonesia faced various insurgent groups, like the Free Acre and East Timor movements but the JI could not combine the Muslim movements under its banner. The dominant factions were ethnic nationalists, tribes and criminals. Local grievances took priority over vague international revolutionary goals that JI and other global Islamists desire.
The Indonesian Government crackdown on JI crippled its headquarters and command structure. Former JI cells are independent or autonomous. The JI regional commanders may be trying to reassert authority, but the Indonesian government must be making life difficult.
Recruiting remained the greatest obstacle. Indonesians mostly don’t care.
The biggest problem Islamic terrorists have had in Indonesia is the opposition from most Moslems there. Islam morphed a bit in Indonesia, as it did in most nations (especially those very distant from Arabia, where Islam was born). Indonesian Islam was never all that hard core, and retained many aspects of pre-Islamic religions. This enrages conservative Moslems, whether they be Indonesian, or from abroad. But attempts to get Indonesians to adopt foreign versions of Islam only appeals to some of the urban hipsters. Many of them are now sitting in jail, or under police surveillance, for getting involved in terrorist activities.
The Nahdatul Ulama of Indonesia is the largest conservative Sunni organization in the world. It has about 40 million members and represents the traditional religious scholars. It staunchly opposes the radicalism and violence of JI, Al-Qaeda, and other radical Islamist movements.
There are four traditional schools of Sunni shari’ah: Hanafi, Maliki, Shafi’i, and Hanbali.
The Indonesians practics a different type of shari’ah than most Arabs. I may have missed a few nuances, but this is what I understand to be the case. The Shafi’i legal school uses jurisprudence and consensus of religious scholars, like the other schools. It is more accomodating to local tribal laws. As Muslims practiced Shafi’i at the fringes, the legal consensus often adopted elements of pre-Islamic tribal laws and customs, making the legal tradition fairly liberal and flexible. This eased conversions and social transitions. Shafi’i incorporates Arabic, shari’ah, and tribal laws and is practiced in South-East Asia, Africa, and Kurdistan.
Radical Islamists, especially Wahabbis, strongly oppose the ‘corruption’ of Islamic law with pagan tribal laws. The really radical ones want to abolish the separate legal traditions of sharia entirely, and establish a single unitary school.
In the end, the ulema (religious scholars) of Indonesia have a vested interest in opposing radical Islam. Most rural Muslims have no interest in this form of radicalism either.
The only ones interested in this are those “urban hipsters.” They’re young, frustrated, university students who fell in love with an absurd fantasy ideology and are willing to kill on its behalf. They’re not much different from the radical Communists in Western Universities.