Hugh Hewitt has written an important article entitled Real Religious Intolerance. In the article, he provides a speech by American Roman Catholic Archbishop Chaput that is worthy of reading in full:

The Los Angeles Weekly’s “The New Blacklist” is author Douglas Ireland’s attempt to equate consumer boycotts of gay-themed entertainment sponsors with McCarthyism.
That’s a stretch to begin with…
Ireland’s piece is full of over-the-top rhetoric, including repeated use of the term “Christers,” which many view as nakedly bigoted.
But Ireland is a proud radical atheist, as blogger-theologian Mark D. Roberts discovered as he began a lengthy assessment of Ireland’s piece…the harshest language in his article didn’t come from him, but from the associate dean of the University of Southern California’s Annenberg School of Communication, Martin Kaplan. Kaplan, a long-time Democratic activist turned professor, called the trend among Christians refusing to buy products advertised on shows such as Will & Grace, “”theocratic oligopoly.” Dean Kaplan continued: “The drumbeat of religious fascism has never been as troubling as it is now in this country.”
Kaplan’s absurdity would have lacked the context to make it other than the silly excess of a tenured Trojan had the Organization for Cooperation and Security in Europe not just held a conference in Cordoba Spain on the rise of anti-Semitism and other forms of religious intolerance in Europe…an American delegation attended…Among the delegation was Denver’s Archbishop Charles Chaput. Archbishop Chaput’s remarks deserve widespread distribution…
Because Dean Kaplan’s bigotry and historical amnesia is not unique, we reprint the entire text of Bishop Chaput’s remarks here:

For a few weeks two months ago, the City of Rome doubled in size. People from around Europe and the world came to the funeral of Pope John Paul II. Some 600,000 people viewed his coffin on the first day. More than 1.4 million paid their respects before his burial. That should remind us of two things.
First, Europe remains obviously religious–not simply in its nominal and active believers, but also in its culture and assumptions about the dignity of the human person.
What we know as “Europe” was shaped, in vital ways, by the Christian faith. Judaism and Islam also clearly made important contributions to the European experience. But the founders of the European unity movement were all professed Christians. Their commitment to the great project of Europe’s future came from their moral convictions, which in turn grew out of their religious identity and Christian heritage.
Second, John Paul II’s appeal to people of every faith–and no faith–did not come simply from his personality but from his actions. His devotion to human freedom and his role in liberating Eastern Europe were rooted completely in his Catholic faith. In one sense, he embodied the greatness of Europe. And he did it by being a son of Europe’s Christian imagination and history.
We know from the totalitarian regimes in Europe’s recent past that a determined minority can persecute other minorities, and oppress even a majority of a nation’s citizens. Discrimination and intolerance toward Christians and minority religious groups are rising in several areas of the world today. Europe, despite its heritage, is not immune. And unfortunately, other parts of the OSCE region show similar troubling signs.
Discrimination and intolerance take two forms: direct and indirect. Direct discrimination has the shape of legal restrictions, and often police harassment and legal barriers, designed to stamp out unauthorized or unpopular religious communities or to limit the legitimate exercise of their religious freedom. The intolerant behavior of some OSCE states continues to violate the basic human rights of belief and worship.
In several OSCE states, regimes discriminate against religious communities by creating structures of prejudicial treatment. High membership requirements prevent small congregations from obtaining legal status which, in contrast, is granted to other “traditional” religious communities. Lack of historical presence can block newer religious groups from qualifying for basic rights and privileges. Denial of legal standing has the very real consequence of either violating individual rights or stigmatizing entire groups. This is state-sponsored discrimination, and it violates OSCE commitments to promote religious freedom for all.
An equally dangerous trend now dominates other OSCE states, where public expressions of religious faith often seem to be ridiculed as fundamentalism. In the name of respecting all religions, a new form of secular intolerance is sometimes imposed. Out of fear of religious fundamentalism, a new kind of secular fundamentalism may be coerced on public institutions and political discourse.
At the same time, various media in the OSCE area now often allow symbols of Christian identity, Christian believers and their faith to be publicly abused. Programs like “How to cook a crucifix” and sacramental confessions recorded without the confessor’s knowledge are deeply contemptuous of Catholic believers. This is unworthy of Europe’s moral dignity and religious heritage. Furthermore, it stands in stark contrast to OSCE commitments to promote religious freedom.
Europe has given the whole world the seeds of democracy. Today’s growing anti-religious and often anti-Christian spirit undermines that witness.
As with anti-Semitism, the OSCE must employ its practical commitments on combating discrimination to also fight discrimination and intolerance against Christians and members of other religious communities. Moreover, the OSCE must carefully monitor their implementation.
OSCE participating states must strive to protect Christian communities and other religious groups from discrimination and intolerance. The media should be encouraged to offer truly balanced coverage of religious faith. Educational systems should teach the value of faith in people’s lives. The specific contribution given to public life by Christian communities and other religious groups should be remembered.
Democracy depends on people of conviction taking an active, visible part in public life; peacefully and respectfully, but vigorously. That includes Christians, Jews, Muslims and all religious believers, as well as non-believers. Public debate without a free and welcoming role for religious faith does not produce diversity or pluralism. It can easily do the opposite. It can create politics without morality, and public institutions without enduring ideals.
My hope is that OSCE participating states will do everything in their power to discourage all forms of religious intolerance – including any disrespect for Europe’s own Christian roots.”

As a broader counter-argument to the arguments of the secular left fundamentalists, I would offer the following postings grouped loosely by subject matter:
The Founding Principles of America
Honoring The Land We Love
Our Declaration of Independence
America’s Tainted Public Discourse & Competing Worldviews
Liberal Fundamentalism, Revisited
The Naked Public Square Revisited, Part I
The Naked Public Square Revisited, Part II
The Naked Public Square Revisited, Part III
The Naked Public Square Revisited, Part IV
The Meaning of Tolerance
Respectful Competition: A Basic Requirement for a Healthy Democracy
What Does “Social Justice” Mean?
Coerced Charity vs. Voluntary Charity
John Paul II, Requiescat in pacem
A Poignant Reflection on Pope John Paul II
Pope Benedict XVI: Offering Faith as an Antidote to Relativism
Discussing Justice, Rights & Moral Common Sense
Ideological Problems in Academia
Where is the Moral Outrage?
Where is the Moral Outrage? Part V
Where is the Moral Outrage? Part VI
Public Policy Structural Challenges
Lawrence Reed on “Seven Principles of Sound Public Policy”
Misguided Incentives Drive Public Sector Taxation
Summing It All Up
Discussing the Incivility in Today’s Public Discourse
A Reasoned Alternative to the Ongoing Name-Calling in America’s Public Discourse: Additional Commentary
Rediscovering Civility and Purpose in America’s Public Discourse