Dated a Chinese-Indonesian girl, so have a view on this: There is ongoing discrimination against Chinese people who wish to express their culture. Which is an improvement over the race riots of the past.
They are hated as seen as wealthy through deceit and have to deal with crazy crap like people attacking their pig farms. Which I found hilarious until the same people then began attacking Bali.
As for personal freedom: laughing on public transport was enough for us to be accosted by a stranger telling us 'we don't act like that here'. No touching, no kissing, just lame jokes shared by members of the opposite sex.
Like Malaysia's infamous Kelantan region (from where the anti-Thai attacks are hatched), much of rural Indonesia is full of conservative Muslims who must be appeased. This conservatism is always at war with the secular urban populations. Sometimes it wins.
Try living in the shadow of an Islamic society. It's really really not fun.
I can hardly think of a single Muslim-majority country that doesn't have absurd violations of basic human rights like this one.
If I'm reading it correctly, it says that in Malaysia, 86% of Muslims believe Sharia should be the law of the land, with 62% of those wanting death for apostates. Overall, the global picture of what "Muslims think" is not pretty.