Good question. After googling the topic, I found that it's the Indonesian military carrying out possible genocidal activities, probably at the behest of an arm of the government and for reasons that, in my opinion, aren't religion or race-based. It's about control of PNG resources, maintaining a foothold of power in the region and quelling the PNG separatist movement.
Although Indonesia is the world's most populous Muslim nation I was surprised to discover that other religions are accepted and encouraged to thrive. There are six recognised faiths allowed under law - Islam, Catholicism, Protestantism, Hinduism, Buddhism and Confucianism. What the Indo rulers don't like is Atheism - you can't be an athiest in Indonesia. There are also many places in the archipelago where local, animist religions thrive alongside and mixed the allowed five, particularly in Nusa Tenngarra, the eastern, predominantly Christian part (Flores, Sumba, West Timor).
Back to the question - this is not the first time in history that the Indonesian military has embarked on campaigns against an ethnic population (Timor Leste for example) and it is worth noting that they had the backing of the USA and Australia when they annexed that unfortunate country after the Portuguese colonialists pulled out (reason: to stop the Socialist Government).
It's not as simple as blaming Islam or racism for this - power over and control of resources is of course the reason, as is creating a bulkhead against other expanding powers in the Asia/Pacific reason (China) and in this task they (probably) have the tacit approval of us - Australia and the USA.