You may be confusing Suharto with someone else. I lived in Indonesia for quite a few years during the Suharto years and the type of activity you refer to was very uncommon. Most of the outrages came later, after Suharto was out of power.
Your use of the present tense indicates that you may have Susilo Bambang Yudhoyono in mind.
I lived in Indonesia as an expat for a few years too, and I believe he’s referring to what happened in East Timor and more remote areas. Missionaries and foreign aid workers are very familiar with what horrors happened out there. As expats in Indonesia, most of us lived quite privileged lives and probably didn’t often hear about what was happening on the outskirts. I know that for some time I didn’t. Don’t know if that applies to you, and if it doesn’t, my apologies.
As for the 1998 riots and atrocities committed against the ethnic Chinese there, who knows? Lots of speculation about who might be behind them.