Yes, atheists do suffer persecution, and not only as indicated in the report. They are often despised and mistrusted for no other reason than their lack of belief. Religion is not only ‘expected’, it’s ‘demanded’. The medieval mindset that constitutes law in the eastern countries mentioned in the report is not unexpected, but the fact that an atheist’s testimony is deemed unacceptable in a western court of law is an appalling indictment of the mentality of the law-makers. Religion demands respect, but it is extremely reluctant to extend that courtesy elsewhere.
As for form-filling, people in the western world often tick ‘Christian’ because they’re conditioned by society - it’s the easiest thing to do. As Em says, there should be no requirement for religious preferences to be expressed – but since religion is imposed upon all of us, it’s no surprise that the category is considered relevant and, hence, included.