There’s nothing like an internal critic taking on the most powerful force in his religion.

Roy Bourgeois is an American Catholic priest. He’s the founder of School of the Americas Watch, a group dedicated to closing the US Army School of the Americas – a military training centre for Latin American officers from nations with horrible human rights records. After Pope Francis recently damned capitalism as a “new tyranny”, Bourgeois told Democracy Now! that he welcomed the strong comments, but urged the Catholic head to go much harder:

Pope Francis must simply come out ... and say, we are all created of equal worth and dignity. We do not have this inclusiveness in the Roman Catholic Church. Therein lies the problem ... I highly recommend that our viewers go to the catechism of the Catholic church which talks about the church’s official doctrines and teachings. Some of them, especially dealing with women and homosexuality, I would refuse to read on the air. It is so offensive, it’s so cruel ... The Pope must get serious and start talking about inclusiveness in the Catholic church.

In the same vein, George Monbiot recently damned Pope Francis for whispering some progressive thoughts and throwing bones to liberals desperate to imagine the Catholic hierarchy as open to reform, while still celebrating the worst forms of colonialism and fanaticism. Don’t expect to be welcomed into the highest echelons of Rome if you’re female, openly gay, married or polyamorous. For these reasons alone, the church must be treated with the contempt such views deserve.

But the argument must not end there.

A dangerous trend has developed in the last decade with the advent of the "new atheism" movement – it often states that people in business, politics and entertainment should avoid discussing religion, and how faith affects their lives. According to its proponents, belief is pathetic and tired, anti-intellectual and predictable. Anybody who follows the Qur'ran, Bible, Torah or other holy book should "grow up" and stop following the teachings of old, bearded men from a time when women were little more than ornaments and baby makers.

How terribly wrong and bigoted such advocates are.

I write this as an atheist, anti-Zionist Jew who worries about the conservative religious views of my prime minister Tony Abbott – journalist Geoff Kitney once accurately described him as a leader who presents “brand Australia” as “neo-conservative nationalism with a populist twist”. Abbott’s intervention against abortion drug RU486 and traditional (and often sexist) politics must be repelled and challenged. Australia in the 21st century should strive for gender, sex, religious and pay equality.

All these concerns are valid: religious views must not influence governmental decisions about abortion, reproductive health or gender parity. But too often aggressive atheists, perhaps rhetorically competing with the most militant religious fanatics, argue that religion is a disease that needs a cure. Taking comfort or lessons from religion is a perfectly legitimate way to live life. Private atheism is as harmless as quietly praying in a church, synagogue or mosque. New atheists are always quick to forget that some of the finest advocates for human rights and justice are religious believers.

US atheist philosopher Sam Harris - lover of US imperialism in the Muslim world and Israel - recently praised the Pakistani girl Malala Yousafzai as “the best thing to come out of the Muslim world in a thousand years.” He went on:

She is an extraordinarily brave and eloquent girl who is doing what millions of Muslim men and women are too terrified to do—stand up to the misogyny of traditional Islam.

In his rush to demonise hundreds of millions of Muslims around the world, Harris clearly hadn’t read the words of Malala herself, praising traditional Islam:

The Taliban think we are not Muslims, but we are. We believe in God more than they do, and we trust him to protect us ... I’m still following my own culture, Pashtun culture ... Islam says that it is not only each child’s right to get education, rather it is their duty and responsibility.

Harris and his many followers in the new atheist movement are desperate to eradicate religion from public life – though it's worth noting the vast bulk of their hatred is directed at Islam and not Christianity, Judaism or Hinduism. Unfortunately, it ignores the fundamental tenet of personal, religious belief: on its own faith, isn’t oppressive. It’s the organised nature of law and teachings that can overwhelm and demean. The fact that Malala clearly wanted a devout Muslim life is an inconvenience conveniently ignored by Harris – it goes to the heart of the unthinking, visceral disdain shown towards religious adherents.

We too often poke fun at political leaders who espouse certain religious views only to have a change of heart – like former Australian prime minister Kevin Rudd, who reversed his position on gay marriage and arrived at the conclusion that it was un-Christian to discriminate against gay couples. This shows there is place for debate and U-turns in religion – and surely this is something to be welcomed.

The ideal secular nation is one where people of all faiths, or none, believe that everybody is encouraged to not feel ashamed of public displays of faith. The richness of humanity, after all, lies in the desire to avoid sterility and uniformity.

An atheist utopia sounds like a nightmare on earth.