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I agree, but at the same time I think it would be true to say that Islamophobia is a particular problem. Nobody has felt the need to coin the word Sikhophobia yet.
The two potential examples you are quoting are very extreme and it would be fairly ridiculous if they were considered to be hate crimes because they are, as you suggest, about free Speech. Surely this is more about if you beat someone up or do something else to someone BECAUSE they are a Muslim...