It is democracy and free speech that is enabling Islamic politics in Indonesia. The alternative is a strongman who imposes secularism. Indonesia already tried that, it is not so good for minorities.
Indonesia doesn't have free speech. Look what happened to Ahok. The FPI, who wants to institute sharia law, managed to get him jailed for two years on a BS blasphemy charge. Where is the "atheism" option for the KTP?
I'm afraid the concept of separation of Church and state in the Indonesian constitution and principles is not nearly strong enough. It's trying to have the cake and eat it too. I don't believe the legal constructs and government checks are strong enough to resist what's coming.
