http://www.straitstimes.com/Breaking...ry_662225.html

'I have witnessed that there has been a radicalisation movement in this nation with religious and ideological motives,' Yudhoyono said in a speech at a national development conference in Jakarta. 'If we continue to let this happen, it will threaten the character of our nation and our people.'

Yudhoyono has allied himself with conservative Muslims in the government and has rarely spoken out against extremist violence, which often goes unpunished.

But on Thursday he said Islamic extremists, who make up a small but very vocal section of Indonesia's 200 million Muslims, were encouraging young Indonesians to 'love violence' and reject the law of the diverse country
http://www.thejakartaglobe.com/home/...469669#Scene_1

Radicalism Losing Ground in Indonesia but Not in Universities: Survey

Support for radicals and radicalism is falling among Indonesians, a survey of 4,840 people has found. The survey by Lazuardi Birru, a Jakarta-based peace group, used a one-to-100 point scoring scale based on answers to a questionnaire, with one being most moderate and 100 being most radical. It measures respondents’ support for radicals as well as their own radical tendencies.
Zuhairi Misrawi, chairman of the Moderate Muslim Society, said support for radicalism may be declining, but the fact is that the number of incidents has been rising, partly because punishments for those who are caught are so weak.

“These non-deterrent punishments have boosted the confidence of the radicals,” Zuhairi told The Straits Times. “It indeed encourages future acts.”
As for the Bojinka Plot, I know it was "compromised" in Manila, but suspect that like the 9/11 plot it was conceived over time in a lot of places to include Malaysia, Saudi, Pakistan, and maybe even during meetings in Mindanao. The good news is it was disrupted.

My biggest concern in the Philippines isn't the ASG, but rather the Balik Islam movement and the potential pool of recruits throughout the Philippines to include Manila that could truly conduct strategic attacks.

You're right that JI and its off shoots have not evolved into an insurgency, but there are still reasons for concern. Det 88 has done a great job at suppressing the threat, but the ideology is alive and well among the true believers (even if they are a minority).