There are quite a few things that are wrong with them but Islam is not one of those things. There are 200m Indonesian Muslims and there 350m Muslims who speak an Arabic language. How many Indonesian terrorists do you know?
Bar the Bali bombings of course, there are some attacks, not many.
The Indonesian government made a policy change under the previous president, and that has persisted with the current one.
Their response teams do 'raids' on the various cells when discovered.
Unfortunately, when these raids happen, every single terrorist seems to be killed, every one, every time they raid.
It saves having to put them on trial. The previous trial, where the Bali bombers were convicted then executed was a PR disaster, as the half witted and fully witted bombers talked at length, smiling, about heaven and the virgins who awaited them upon their death.
It generally sickened the Indonesian people, who for the most part, especially in the main populaces are moderate. So the decision was made to try to minimise any further trials and execute at the point of raid, where it could be explained away as a firefight. These raids happen reasonably regularly.
It isn't quite as good for the world stage as back when hey were ruled by dictatorship, as any preacher or cleric who spoke out of turn back then was later discovered by a farmer in his rice field (and quickly reburied), but it is more towards democracy, and seemingly just (depending on your viewpoint).
