Yes, there are, at least demonstrably.
One such group is the Ahmadi minority within Islam. Very briefly, I'll say that Ahmadis believe that the Prophet Muhammad was not the final prophet sent by God, that there was still another one, but in most other ways, Ahmadis do identify as Muslim. A war, really, has been waged and continues to be waged against Ahmadis, in killings, targeted killings, in shootings, and other forms of oppression throughout the country.
Then there is the denomination known as Shia Muslims. They, too, in the vast scope of the Muslim world, are a minority. I won't get into the theological differences, but another war is being waged against Shias, so much so, by the way, that just as is happening with Shias in Pakistan, many people have observed that Indonesia has eerily replicated Pakistan in how it is treating its own Shia Muslims.
Finally, of course, there's the wider group that one would call liberals—small-l liberals—independent-minded Muslims who treasure secularism, who treasure the separation of organized politics from organized religion, and who want that back, for exactly this reason: because Indonesia itself, as a state, is premised on what are called the Pancasila principles, the five Pancasila principles, of which diversity is one, and that diversity of thought, of expression, of conscience, ought to be respected, since this is what Indonesia is supposed to be about.
Let me be very clear: nobody is saying that those who are more fundamentalist in their beliefs have to be expunged, not at all. That's also part of diversity. What they're saying is that imposing those beliefs on people who don't want them is a violation of the constitution, and in that, quite simply, they are correct.
