Obviously there are quite a few things going on here.
There is a lot of hoaxing and religious agitation via social media, which is not really kept under control.
For example the sound of the azan is typically (in Indonesia) blasted out of very poor quality speakers from a recording. This to non-Muslim ears may sound quite horrible, especially at 5am through your bedroom walls. Non-Muslims (and some Muslim) may complain, but are told things like 'we are taught that anyone who doesn't like the sound of the azan must be a devil'.
A woman of Chinese Buddhist ethnicity in Sumatra complained about the sound of the azan and the result of that was riots and burning down of temples. www.jakartaglobe.beritasatu.com/news/angry-mob-burns-monasteries-temples-north-sumatra/ Prosecutors are recommending 18 month prison sentences for her, while the rioters got 1-4 months www.thejakartapost.com/news/2018/08/14/prosecutors-demand-1-5-years-for-buddhist-woman-on-azan-blasphemy-charge.html
In another part of Sumatra mobs burned down churches, to which the official response was for the government to knock down more churches. www.reuters.com/article/us-indonesia-aceh-violence-idUSKCN0SD0H220151019 (The official justification being that the churches lacked building permits, which the local government would never have granted due to pressure from Islamists.)
There is a massive amount of religious hatred stirred up among poorly educated and religiously brainwashed peasants. The recent North Sumatran gubernatorial election had a choice between former Mayor of Jakarta Djarot Hidayat, a fairly capable politician (and Muslim who had completed the Hajj), with deputy Sihar Sitorus, a Christian who was wealhy from palm oil, and Edy Rahmyadi, a rather unpleasant former general, whose deputy was Musa Rajekshah, the son of a famous mafia leader.
While Musa is a very unsavoury character, he had made himself the head of the mosque building committee for the city of Medan, promising to build the largest mosque in Asia, which is under construction.
So the election the election was framed entirely as a choice between Muslim and non-Muslim, even though both candidates were in fact Muslim. Videos were shared on social media explaining the consequences of choosing a non-Muslim (eternal torment in this life andbeyond), and how the prohibitions in the Koran against appointing a non-Muslim as leader are far stricter than those against sins such as eating pork or consuming alcohol.
This was exacerbated by the fact that Djarot had previously been the deputy mayor of Jakarta, to Ahok, the ethnically Chinese Christian who sits in prison on bullshit blasphemy charges (essentially he referenced the Koranic verses used to prohibit non-Muslim leaders). www.theguardian.com/world/2016/dec/12/jakarta-governor-ahoks-blasphemy-trial-all-you-need-to-know Ahok has refused remand, presumably because in the run-up to the 2019 election it was felt that his being released from prison would be used as ammunition against his former colleague President Jokowi, who faces Prabowo a vicious former army leader who loves Nazi imagery, and was essentially trying to exploit Islamism to defeat Jokowi.
Jokowi for his own part appears to have at least to some degree abandoned pluralism, having last week chosen as his running mate the head of the Indonesian Ulema Council, the body responsible for recommendations such as how long to lock up Ahok for, or the Chinese woman above, or indeed on a regional level telling the government to stop issuing MMR vaccines on the basis that they do not have halal certificates.
It is not clear if Indonesia will go down the road of Pakistan, where Imran Khan, drug user, fornicator (and according to his ex-wife in a recent salacious book) and bisexual, is now Prime Minister having tacked hard towards Islamism and being rewarded royally. www.thecricketmonthly.com/story/1154531
Anyway, there is a context in that there is in much of the world no right to free speech or criticise religion, no presumption that liberal thought and free expression is the ultimate good, and in many Muslim-majority parts of Indonesia an overriding presumption that Islam (which is often aggressively defined by Ustad) should inform public life, despite the constitution declaring that there is one Almighty God but a choice of religions (including Hinduism, Buddhism, Protestantism, Catholicism & Confucianism).
Hoaxers spread the idea that there are forces posing an existentential threat to Islam (such as videos claiming that there is a 'rapidly spreading church [the Syriac Orthodox Church] appropriating Arabic language, Muslim styles of prayer, clothing, etc), even where in many areas the Muslim population is in excess of 98%, and there is no real change in the balance between religious population.
So there is a sort of formented hatred engendered which leads to the likes of the church bombings, and consequent resentment among the Christian minority, who resent for example being subject to the (continuing) corrupt leadership of a former general as opposed to a credible poilitician with national profile, resent being subject to restrictions on selling pork, owning dogs, etc.
Many many people are clearly convinced that the likes of the kindergarteners in jihadi costumes are symbolic of a real armed struggle (there is constant reference to Palestine, often again with fake hoax stories, lots of Sinophobia and spurious references to Communism), and would not perceive for a moment that they were being manipulated in order that their leaders continue to steal and enrich themselves, as they see these things religious imperatives as very real from a very real God, in a country where most people don't just have a vague belief in some sort of wishy-washy afterlife, but a day-to-day belief in supernatural events. (Videos on Facebook show a 'Palestinian' (of course) walking on water, a flying palm tree (actually a stunt for a movie, suspended by helicopter), with lots of 'praise Allah' comments from those reading.)
When day-to-day life is not at all based in rational thought then religious fanaticism can become all the more powerful.