Some people, such as Juan Cole, are puzzled by the Malay response in West Malaysia (various protests and six churches either burned down or attempted to be burned down), noting correctly that in most other parts of the world, God and Allah are used interchangeably; for example, Arab Christians refer to God as Allah. However, this linguistic analysis, as correct as it may be, is not the point. The issue at hand is something completely different:
With all due respect to Dr. Cole, I do believe he is missing the point. His linguistic analysis of the word Allah is correct; however, that is not the issue at play in Malaysia.
The real issue at hand is with respect to conversion to Christianity. The Malaysian newspaper in question, The Herald, is published by the Catholic Church. That newspaper is published in several different languages, but the paper written in Bahasa Melayu, the Malay language, is only distributed to the Malaysian states of Sabah and Sarawak, on the island of Borneo. The problem as Malays in West Malaysia (the Malayan peninsula) see it is that the Malays and aboriginal people in East Malaysia are less educated, who lead simpler lives*, and they might become confused in reading a Christian newspaper that prints the word Allah, thinking that The Herald is a Muslim newspaper when it is not. This is a valid concern. IMO, the arguments made by The Herald are smoke screens, trying to hide the newspaper's ulterior motive which, indeed, is to convert people to Catholicism. This is what is making some people so angry that they are committing arson against various churches. As a Muslim, I don't condone this behavior, and I think the Malaysian government and political parties have responded properly to this situation. However, I do think the Catholic Church in Malaysia is being provocative and somewhat disingenuous. IMO, they share some of the blame for what has gone on so far.
* In all fairness, the same argument (not well educated, simpler people) applies to many Malays in West Malaysia as well; however, between the two sides of the country, West Malaysia is more advanced.