His opinion is just one among many. Most Chinese don't have strong opinions of Indonesia. Even those aware of 1998 massacre know that in unstable developing countries, ethnic riots can break out at any time and can target any group, not just Chinese.
Anyway, it's quite obvious that Indonesia needs more Islam. After all, it's not a nation-state, based on any ethnic group. Instead, the state's foundation and legitimacy comes from Islam. If the Indo govt. is too secular, Islamists will become resentful and resort to even more radicalism. I think they need to be accommodated further and see more representation in government.