It’s actually a bit more complicated. The Islam traditionally practiced in Indonesia has been well known for being comparatively tolerant and for promoting pluralism. So the issue is not the fact of being predominantly a Muslim country in itself, but growing influence coming from conservative forces in the Middle East (which, indeed, is not all that surprising).

The largest Islamic organization in the country and traditionally the biggest proponent of a moderate Islam, Nahdlatul Ulama, is clearly naming the problem: Wahhabism. "It is false and counterproductive to claim that the actions of al-Qaeda, ISIS, Boko Haram and other such groups have nothing to do with Islam, or merely represent a perversion of Islamic teachings. They are, in fact, outgrowths of Wahhabism and other fundamentalist streams of Sunni Islam," Yaqut said." http://www.thejakartapost.com/news/2017/05/25/humanitarian-i...

Interesting read about the same topic here http://foreignpolicy.com/2017/02/14/indonesias-moderate-isla...

It's definitely sad to see the moderate forces lose against the foreign-funded supporters of extremist views in what otherwise is a beautiful country.