He has recently gone on the record in the Jakarta Post as saying that the attacks by the FPI on 1 June 2008 were sure to be a challenge for the government in ensuring that people from other countries did not develop the wrong perception of Indonesia as an intolerant country.
According to Magnis-Suseno the idea that the FPI represents mainstream Indonesian Islam is nonsense and something that must be addressed sooner rather than late if the Indonesian government is serious about averting the spread of this misconception.
Nevertheless, he did acknowledge that the attack of 1 June is an indication that there is violence lurking just under the surface and that it can explode into open violence at any moment. There was also an acknowledgement that the government is often paralyzed by the fear of being seen as anti-Islam or pro-Islam (I would suggest the pro-Islam issue is one of being seen to be pro-radical or fundamental Islam) that it tends to act slowly or do nothing.
The reality is that people identify as Muslim first and Indonesian second and this simply means they put the interests of their religion ahead of the interests of their country. This is in part why Islam has been so successful in spreading and thriving throughout the world as all interests are secondary to the practice of the religion.
It is interesting to read the words of Nadya Madjid, the daughter of one of Indonesia's foremost Islamic scholars, Nurcholish Madjid or Cak Nur, who makes the analogy that Indonesian Islam is in the puberty stage. This is to mean that it is still trying to find its identity as it moves into adulthood. This is both hopeful and scary as the potential remains that Indonesian Islam may still take a sharp turn to more fundamental interpretations of the Qur'an.
Such is Life!