Indonesia went through several different phases throughout its history.
Since the arrival of their ancestors from South East China (or somewhere around the area), they have dispersed throughout the archipelago, forming small tribes that later evolved into other sub-tribes. Note that regional population patterns were already established around this time. These patterns are still applied in the present day, almost like territories.So for example, the Sunda people dwell on the west region of Java Island, Batak people dwell on the north region of Sumatra Island, Bali people dwell in Bali Island, etc.
Around 6th century AD, the first wave of major culturisation hit Indonesia. It was Hindu culturisation, later also followed closely by Buddhist. These were the results of trades and diplomatic relationships with kingdoms of the Far East and Indian subcontinent, hence it was known as Indochina for quite some time. Many great kingdoms are built under Hindu culture, giving birth to advanced civilisation that becomes very famous throughout Asia. Borobudur temple (was once one of the seven wonders of the world) is the most renown remain of this era.
Around 13th century AD, Islam culturisation arrived at the north coast of Sumatra (Aceh) and Java, also by means of trades done by businessmen from Saudi Arabia and the Gulf kingdoms (Ottoman empire). After generations of inter marriages with local women and the royal princesses of these kingdoms, some of the kingdoms were succesfully converted into Islam. The Islam influence was later followed by Christian influence from the colonialisation by European empire. But because of the regional pattern established early on, some places remained intact and not influenced by the waves of culturisation. Bali is immune towards Islam influence. North Sumatra (Batak region) on the other hand, is one of only a few areas dominated by Christian influence. Some tribes in Papua still live from animism and dinamism, meaning they are resistant towards all Hindu, Buddhist, Islam, and Christian influences.
The point is that complete culturisation is impossible to achieve in such a vast archipelago. There are always barriers that prevent homogenisation to happen in such a diverse nation whose tribal traditions went back to the dawn of time.
P.S. Indonesia might have the greatest Muslim population in the world, but the constitution acknowledges 5 different religions and all traditions under its sky. So it might not be correct to call it a Muslim nation. To date, it is still a diverse nation that believes in its national motto ‘Bhinneka Tunggal Ika’ (note this motto is using Sanskrit, which is an ancient language of India) or translated as ‘Unity in Diversity’.
I’m Indonesian, a Chinese descendent (or Tionghoa as they call it in Indonesia), have been living in Indonesia for 18 years (and on/off between Indonesia and the UK for the past 2 years), a Buddhist, have Sanskrit middle and last names, can recite the Islamic daily prayer (because it’s always on TV during the praying hours), went to Catholic schools for 12 years, know Arabic, and celebrate Chinese New Year in all its glory every year.