It's a minority. That much is clear. You just walk around Java and you can see that it is not a particularly conservative place. It's not like walking around Quetta, Pakistan, or Kandahar, Afghanistan. It's certainly the case that extremist views, Salifist views, radical or extremist Sunni views, are not the majority opinion of most Sunnis in Indonesia.
It's not just a couple of people either. These are large, well-funded, very extremist groups that have increasing amounts of political power. So while they're not the majority, they're also not insignificant. It's not just a couple of thugs; it's actually some very disturbing and very powerful political parties with quite a lot of people behind them.