Did you ever read about what they did to East Timor?
East Timor was a territorial issue and totally unrelated to Islam indeed as I recall the US fully supported Indonesia taking over East Timor to prevent it falling to the Communists.
Rest assured if you were a Christian and you had to pick the safest Muslim majority country in the world to live in Indonesia would be very near the top of your list as opposed to the US created Islamist hellholes in Iraq or Afghanistan or for that matter the US’s “good friend”(quote: George W Bush) Saudi Arabia.