Islamic radicals continue to push their anti-Christian policies using violence. The government generally backs off as long as no one is killed or property is not destroyed. The government does not want to be seen as "anti-Islamic" while also not allowing Islamic radicals to gain more power or seem to be running the country. This results in a lot of annoying policies. The government allows thousands of Islamic radical men to go around in groups (usually of a few dozen) who use intimidation, and sometimes physical force, to shut down what they consider "un-Islamic" behavior. While police refuse to stop this mob action against night clubs or Christian churches, the police will also look the other way if locals get together and confront the Islamic radical mobs.
Many Indonesians, including most Muslims, are unhappy with the tolerance for Islamic radicals. But the government believes keeping the Islamic radicals out in the open makes it easier to prevent Islamic terrorism. The government seems to have captured, prosecuted, and jailed most major Islamic terrorists in the country. Few Indonesians want a return to the bad-old-days. For example, between 1999 (when the decades old dictatorship was overthrown) and 2002, newly liberated Islamic terrorists killed over 6,000 Indonesian
Christians. That was largely suppressed by 2003, but the Islamic terror groups continued with bombings and other small attacks. That took several more years to deal with. Now it's all a question of when, or if, the Islamic radicals will escalate their violence to a level that will trigger a major backlash by Indonesian Muslims. If past history is any indicator this could get very nasty, which is something else the government has to keep in mind.
While 13 percent of Indonesians are not Muslim, these Christian and Hindu communities are concentrated in a few areas making it easier for most Indonesians to ignore the ugly antics of the Islamic radicals. But as these same groups increasingly harass other Muslims the push-back increases.
In Papua the police and army continue skirmishing with armed and unarmed separatists. There are casualties every month but not enough to grab global media attention. The separatists are not making much progress.
July 16, 2012: Counter-terrorism police from Indonesia and Singapore completed three days of joint exercises. This is part of a larger program to foster close cooperation with neighboring countries (including China) in anti-terrorism matters. Mostly this involves sharing information, but increasingly it involves personnel training together and exchanging techniques.
Asian Defense News