'If you're not religious, for God's sake say so," we implored, and many did. Over a quarter of the population registered as non-believers: more might have done were the census question unambiguous about whether it meant cultural background or personal belief. My term as president of the British Humanist Association ends this month, but gladly I hand over to Jim Al-Khalili, the distinguished professor of physics, writer, broadcaster and explainer of science. With atheism as the second largest block, he will be in a stronger position to see that unbelievers get a better hearing.

Rows over gay marriage and women bishops bewilder most people. With overwhelming popular support for both, how can abstruse theology and unpleasant prejudice cause such agitation at Westminster and in the rightwing press? Politics looks even more out of touch when obscure doctrine holds a disproportionate place in national life.

The religions still frighten politicians, because despite small numbers in the pews, synagogues and mosques, they are organised and vocal when most of the rest of society lacks community voice or influence. Labour was craven, endlessly wooing faith groups – David Blunkett wishing he could "bottle the magic" of faith schools.

With a third of state schools religious in this most secular country, Michael Gove not only swells their number but lets them discriminate as they please in admissions. As he is sending a bible to every English school, the BHA is fundraising to send out its own Young Atheist's Handbook to school libraries. Government departments are outsourcing more services to faith groups in health, hospice, community and social care.

But of all the battles Jim Al-Khalili confronts, the most urgent is the right to die. Powerful religious forces block attempts to let the dying end their lives when they choose. Tony Nicklinson was the most public face of thousands in care homes and hospitals condemned to what he called "a living nightmare" by 26 bishops and other religious lords who say only God can dispose – the Bishop of Oxford decreed: "We are not autonomous beings." The public supports the right to die, but many more will drag themselves off to a bleak Swiss clinic before the religions let us die in peace.

Sensing the ebbing tide of faith since the last census, the blowback against unbelievers has been remarkably violently expressed. Puzzlingly, we are routinely referred to as "aggressive atheists" as if non-belief itself were an affront. But we are with Voltaire, defending to the death people's right to believe whatever they choose, but fighting to prevent them imposing their creeds on others.

The Abrahamic faiths, with their disgust for sex and women, still exert deep cultural influence. When David Cameron claimed "we are a Christian country", there are certainly enough cultural relics in attitudes towards women and gays. Baroness Warsi's letter expressing alarm that schools might teach gay marriage equality causes tremors of that sexual disgust branded into the souls of all three major monotheistic faiths. Are there many gay couples perverse enough to yearn to be married inside religions that abhor them? Humanists can offer them heartfelt celebrations.

In the Lords this week, by a whisker, section 5 of the Public Order Act was amended to remove the offence of using "insulting words or behaviour within hearing or sight of a person likely to be caused harm, alarm or distress thereby".

An extraordinary alliance of extreme religions wanting the right to preach fire and brimstone against gays joined with free thinkers wanting the right to be rude about religions. Liberty and the Christian Institute were on the same side against the government, which was defeated. Now the Commons will have to decide. Some religions argue they have a God-given right not to be caused offence, to give legal weight to fatwas against those who offend their prophets. But in the rough and tumble of free speech, no one can be protected against feeling offended. Jim Al-Khalili can expect all manner of attacks, but no protection for his sensibilities.

For instance, he might take offence at the charge that without God, unbelievers have no moral compass. Hitler and Stalin were atheists, that's where it leads. We can ripost with religious atrocities, Godly genocides or the Inquisition, but that's futile. Wise atheists make no moral claims, seeing good and bad randomly spread among humanity regardless of faith. Humans do have a hardwired moral sense, every child born with an instinct for justice that makes us by nature social animals, not needing revelations from ancient texts. The idea that morality can only be frightened into us artificially, by divine edict, is degrading.

The new president will confront another common insult: atheists are desiccated rationalists with nothing spiritual in their lives, poor shrivelled souls lacking transcendental joy and wonder. But in awe of the natural world of physics, he'll have no trouble with that. Earthbound, there is enough wonder in the magical realms of human imagination, thought, dream, memory and fantasy where most people reside for much of their waking lives. There is no emotional or spiritual deficiency in rejecting creeds that stunt and infantalise the imagination.

Liberated by knowing the here and now is all there is, humanists are optimists, certain that our destiny rests in our own hands. That's why most humanists are natural social democrats, not conservatives.