ACEH: which side are you on?

I don't know too much of the particulars but it seems like a case of an ethnic & religious minority (in this case Christian) living in a certain region (Aceh) wanting to be independent of the central government which is located on a different island (Java) and tends to be dominated by different groups (primarily Muslim). I could be way over-generalizing and/or wrong about any part of that. So on the one hand I'm sympathetic to the separatists wanting to have autonomy, but on the other hand, I ask myself, where will it stop? Indonesia is made up of hundreds of little islands with different ethnic groups, and if the country is to survive at all as a country then it's going to have to insist on some unity. Especially now that Indonesia is becoming a functioning democracy, I think it would be ideal if Aceh could find a way to achieve satisfactory representation in the government through regular democratic means. However, as I mentioned in my initial caveat, I really don't know too much about the history and particulars of this one.