Paul Fidalgo is communications director of the Center for Inquiry, a nonprofit educational, advocacy and research organization. The views expressed in this commentary are solely those of the author

(CNN) In recent days, Pope Francis has talked a lot about tolerance and freedom of conscience. But he has failed to distinguish between those who truly suffer from persecution and discrimination and those who claim to be persecuted when told they may not discriminate.

True prisoners of conscience are even now suffering punishments grotesque and medieval for exercising their right to criticize religion. But during his visit to the United States last week, the Pope chose instead to focus his attention and sympathies on a government employee who decided that her faith trumped her legal obligations and the constitutional rights of others.

Pope Francis met secretly with Kentucky county clerk Kim Davis, who refused to sign off on marriage documents for same-sex couples, citing religious objections. Speaking to journalists on the plane back to Europe, Francis explicitly endorsed this kind of discrimination, calling it "conscientious objection" and a "duty."

But what does the Pope have to say about atheists and secularists who have been jailed, attacked or killed for expressing their own conscientious objections to religion?

Nothing.

Instead of defending those who have lost their basic human rights, he wastes his political capital on those who seek to deny rights to others.

If he truly wants to defend the right of human beings to follow their consciences, he could speak out on behalf of the persecuted atheists and secularists who languish in captivity or mortal fear for expressing their sincerely held beliefs.

He could use his global megaphone to speak on behalf of the right of people not to believe, and to criticize faith -- any faith, including his own.

Right now there is a brutal crackdown on free expression and religious dissent going on in countries such as Pakistan, Saudi Arabia, Indonesia, and Bangladesh, among many others.

Secularists in countries such as these face a kind of persecution that is not limited to marginalization or censorship but includes incarceration, floggings and even death.

Civil servant Alexander Aan expressed his atheism on Facebook, and in 2012 was attacked by a mob and then himself arrested and jailed for his blasphemy.

In 2013, Raif Badawi in Saudi Arabia was convicted of "insulting Islam" for running a liberal website that questioned tenets of the faith. He is serving a 10-year prison sentence and waits for his next installment of public lashings, having now endured 50 of the 1,000 to which he was condemned.

And penalties of death come either via the state, such as in Pakistan, where blasphemy is punishable by death, or by radical extremists, who murder in the streets with impunity.

Such has been the fate of no fewer than four atheist bloggers in Bangladesh this year alone, including Avijit Roy , the Bangladeshi-American writer who was waylaid at a Dhaka book fair by Islamists with machetes in February.

Francis missed several opportunities while in the United States to speak up for these persecuted nonbelievers -- for their right to not believe in any gods, to question religious tenets and to express themselves without fear of prosecution or violent retribution.

But it's not too late. He could still urge the government of Bangladesh to take seriously its obligations under U.N. charters to protect the right of free expression and belief for its people, and to safeguard the lives of its people, even those who criticize religion.

After all, today is International Blasphemy Rights Day , an initiative begun by my organization, the Center for Inquiry, to defend free expression and protect dissent.

I would never expect this Pope to be a champion of secularism or nonbelief. But I do hope he discovers his duty to his own conscience and becomes an ally on this critical issue.