Indonesia had its share of issues with foreign influence during the Cold War.
Like many in the Middle East, Indonesians are willing to cheer and support AQ's fight against foreign intervention in Muslim lands. Also like many in the Middle East, they are quite willing to accept help from Islamist movements where their own local issues (traditionally involving sectarian conflict in Sulawesi et al). Also like many Muslims elsewhere, very few beyond a small core want anything to do with the idea of an Arab-ruled Calihate, or with local terrorism, or with the prospect of having an AQ-allied government.
Much of today's Sinophobia seems to me curiously unspecific... people seem convinced that we need to fear China but unsure of what they are afraid that the Chinese will do. I sometimes come away feeling that they simply feel bereft without someone to fear.
One wouldn't want to stereotype, but in general SE Asian Muslims are much less socially conservative than those in South Asia and the Middle East, even in places where Islamic radicalism has a foothold. That of course varies widely with location: an Indonesian Muslim from Jakarta is likely to be a lot less conservative than one from a rural village.
There have been some efforts to impose a more conservative outlook, notably in Malaysia and Indonesia (such as the current proposal to ban skirts above the knee) but the fact that the clerics see the need to try to force such moves is in itself testimony to the reality that the culture does not demand them.
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