I think I read a timeline where one can see that this kind of atmosphere has grown directly in correlation with Saudi (Salafi) investment in Indonesia. I can not be assured that that is a fact.
Indonesia is probably somewhat hospitable to an open society but these stories are worrisome. A friend goes to Malaysia ever so often, similar situation. Muslims are a bit of the over-class there vs. other religions though at this point, it doesn't seem to be outright radicalism ruling.