This week a 23-year-old Afghan man became the first person to be granted asylum in Britain on the basis of his atheism – which, his lawyers argued, would have made life impossible in his country of birth, where religion permeates every aspect of life.

The home office declined to comment, beyond a statement that is both bland and inaccurate by omission: "The UK has a proud history of granting asylum to those who need it and we consider every application on a case by case basis." (It should have read "a proud history that we've abandoned …", but never mind.)

Theresa May probably feared an onslaught of xenophobic remarks – "What could be more specious than a belief that is really the absence of belief, a luxury belief for cynics and intellectuals? What next? Asylum for French people who prefer Derrida to Foucault?" – but the critical comment barely came.

Instead, there was a generalised, muted acceptance, which makes perfect sense. If you accept the place of religious belief on the human rights agenda, then you have to allow atheism equal weight. It is as much a traducement of religious people to dismiss atheism as it is a denigration of atheists.

However, there's a lot of shifting sand around this principle – it is telling that this man is the first atheist to be offered asylum here, when he can't be the first ever to face persecution. Australia accepts the principle of atheism as a belief to be protected, while the United States doesn't. It's one of those things nations can cherry-pick from the fruit bowl of international law without feeling that their "civilised" status is compromised. It may be the only belief of that kind right there in the 1951 refugee convention, but with no backup institution vulgar enough to insist upon it. That is part of our problem, us atheists: we don't organise.

Active unbeliever

But I don't think that failure of organisation justifies the habitually low status of atheism: not just in refugee law, but also across civic life. Now, more intensely than ever – as we see our state education system carved up among whatever faith groups shout the loudest, and whichever crooks pretend a faith – the voice of the active unbeliever is not only unsought but also treated as an irrelevance. Schools are required to take a proportion of children from "other faiths"; atheism doesn't count. Or, if you think it does, try filling in the form where you describe your "other faith" – "I am raising my child to believe you people are mad. Will that do?"

Community groups – whose opinions are so slavishly sought, for about five minutes, after anything blows up in a community, are almost always predicated on faith, meeting in religious buildings, around religious timetables.

Babies are said to be "born Muslim" – this asylum seeker, for instance, was described as having been born a Muslim, and losing his faith as a teenager.

But as Richard Dawkins pointed out in a letter to the Times this week, there is no such thing as a Muslim baby – babies and toddlers being "too young to know what they think about origins, moral philosophy or the meaning of life". Atheism would never be accorded that status.

Of course, faith is often used as a proxy for race: a euphemism for "that baby may have been born here, but it doesn't look very English". At other times religion is used as an open marker for cultural identity, so that Jewish atheists are still described first as Jewish, the atheism being a quirk rather than the Judaism – even though the latter is surely quirkier, a religious identification that conveys no belief.

Lumped together

Atheists are very often lumped in with secularists, although these concepts are nothing like the same. But perhaps most vexingly, while the fine distinctions among the religious are pored over in every survey (are you this kind of Christian or that; are you practising, or do you simply tell people you have a spiritual side?), the most important and exhaustive survey we have on British belief doesn't even ask the question "Are you an atheist?". In last year's British Social Attitudes survey 48% of respondents said they had no religious affiliation. A category that accounted for a third of people in 1983 is now nearly half the population. And nobody thought to ask: "Why not? Did you fall out with organised worship and decide to just ad lib at home? Or do you profoundly believe that you can wring more meaning and beauty from the world accepting it as it is, rather than concocting deities?"

These differences seem important, but even if they're not – even if an on-again-off-again agnostic manifests pretty much the same behaviour as an atheist – they should be distinguished as a matter of courtesy, just as I would accept that there's a difference between Greek Orthodox and Coptic.

This systematic civic exclusion, I think, has rather shallow roots – not in a prejudice against the faithless, but in the loam of human politeness, where groups are accorded attention, respect and sensitivity in proportion to how much they will complain if they don't get it. Something to think about, heathens: maybe we are simply not complaining enough. – guardian.co.uk © Guardian News and Media 2014

Twitter: @zoesqwilliams