The most recent flap involved a lunchtime announcement and subsequent email encouraging cadets to participate in Operation Christmas Child, an annual program of Franklin Graham's Samaritan's Purse relief organization.
"Please consider spending some of your valuable time and money to love on a kid around the world," the email said.
Commanders initially said there was nothing wrong with the academy's involvement in the program, but when pressed further, they apologized and assigned the project to the academy's chaplains who can legally recruit for religious endeavors, The Colorado Springs Gazette reported.
Before that, it was an ethics class on just war theory that was halted because complaints were raised about Scripture verses being used in the course. In February, an annual prayer luncheon drew a lawsuit and caused commanders to clarify that the event was sponsored by chaplains and not the academy.
In November, the Los Angeles Times carried this headline: "Air Force Academy adapts to pagans, druids, witches and Wiccans."
"In the still of a cold November evening, a small gathering of pagans, led by two witches, begins preparations for the coming winter solstice," the article began. "But these are not just any pagans, and this is not just any setting. They are future officers of the United States Air Force practicing their faith in the basement of the Air Force Academy's cadet chapel."
It turns out this year the academy dedicated an $80,000 outdoor "Stonehenge-like" worship center, as the newspaper put it, for cadets with "Earth-based" religions.
"We're here to accommodate all religions, period," Chaplain Maj. Darren Duncan said, noting the current cadet class includes 11 Muslims, 16 Buddhists, 10 Hindus and three pagans as well as 43 self-identified atheists.
Not only does the academy now provide worship space for all, it requires all cadets to complete religious respect training.
Mike Routt, pastor of Circle Drive Baptist Church in Colorado Springs, Colo., told Baptist Press the hostility toward Christianity at the Air Force Academy is not the result of the leadership there but is in response to pressure from Mikey Weinstein of the Military Religious Freedom Foundation.
Weinstein, an Air Force Academy graduate, is described on the foundation's website as "the undisputed leader of the national movement to restore the obliterated wall separating church and state in the most technologically lethal organization ever created by humankind: the United States armed forces."
For a decade, Weinstein served as a military attorney, and he worked in the White House as legal counsel for President Reagan. In 2006, he began focusing his attention on "the nonprofit charitable foundation he founded to directly battle the far-right militant radical evangelical religious fundamentalists."
Weinstein is the author of the book "With God On Our Side: One Man's War Against an Evangelical Coup in America's Military." This year he was named the inaugural "person of the year" by Americans United for the Separation of Church and State.
Routt, who serves on the Southern Baptist Convention's Executive Committee, described Weinstein as a person who angrily threatens lawsuits and pushes unsubstantiated claims on his foundation's website, militaryreligiousfreedom.org.
"He even says the Constitution is to guarantee both freedom of religion and freedom from religion," Routt said, adding that he suspects part of Weinstein's motivation for making outlandish claims is financial gain from those who support his viewpoint.
Weinstein, Routt said, is able to portray Operation Christmas Child in a negative light because his readers are not familiar with the program. In a letter to supporters, Weinstein called it "a project of internationally-infamous Islamophobe Franklin Graham's Samaritan's Purse organization."
"Ostensibly meant to bring a bit of 'Christmas cheer' to children in disaster areas and war-stricken nations, this missionary program masquerading as an innocuous charity uses deliveries of toys and toiletries as a Trojan horse to sneak Graham's fundamentalist Christian ministry of Jesus Christ into 'heathen' nations such as Japan, Libya, Haiti and Iraq," Weinstein wrote.
The Military Religious Freedom Foundation believes religious freedom "takes on an additional importance in the current international environment, where religious motivations are an increasing rationale for waging conflict."
"At a time when the United States is encouraging greater religious freedom in Muslim nations, it is imperative upon America to show by example that religious pluralism is a viable and preferred option," the website says. "Any sign of hypocrisy in United States policy, official or otherwise, toward the free exercise of religion within the military makes it more difficult to convince others to follow our nation's chosen path."
Routt reiterated that the recent developments regarding religion at the Air Force Academy "are not the result of inner workings of the leadership there."
"The Christian community in Colorado Springs really embraces the Air Force Academy. There are a lot of wonderful Christian people there, and all of this stuff that's happening at the Air Force Academy I can assure you it's not coming voluntarily from the inside but decisions that are being made due to the pressure from Mikey Weinstein and his organization," he said.
"... The evangelical leaders of our community see these actions as a reflection of the continued secularization of our culture. We understand that as our culture becomes increasingly secular, attacks against biblical Christianity will increase," Routt said.
Daniel Heimbach, a professor of Christian ethics at Southeastern Baptist Theological Seminary in Wake Forest, N.C., told Baptist Press that the Operation Christmas Child reversal is understandable because the program genuinely does promote Christianity and should be handled by the chaplains.
What is most concerning is criticism of the just war class, said Heimbach, who has worked in defense- and domestic-policy positions in Washington in both the executive and legislative branches.
"That the western tradition of just war ethics has included biblical as well as classical influences is simply a matter of history," Heimbach said. "Although academy courses are no place for religious indoctrination, neither should they deconstruct what actually has occurred as though religion does not exist.
"Teaching of the history and development of just war history should be fair and objective whether at a military academy or at a religious seminary."
Weinstein's interpretation of the U.S. Constitution "has no historical basis since he aims to restore something that has never yet existed," Heimbach said, referring to the freedom from religion claim.
"The same men who ensured our Constitution would guarantee freedom of religion also ensured that religious chaplains would be hired at taxpayer expense to serve with civil institutions," Heimbach said. "Doing that is compatible with and even required by freedom of religion and is problematic only by supposing the Constitution assures freedom from religion."
Regarding the outdoor worship center for cadets with "Earth-based" religions, Heimbach stated that the Air Force Academy "should be a place where the religious life of all cadets is respected without hindrance, bias or favoritism. And yet something is grossly out of proportion when the institution dedicates a $80,000 outdoor worship center to only serve 3 cadets. That is because only pagan cadets fall in this category and the academy only has 3 pagan cadets. Along with Christianity and Judaism, Islam, Buddhism and Hinduism also are not 'Earth-based' religions. And while Atheism is a religious category, it entails no ritual practices of the sort that require huge outdoor worship centers. All of which leads me to wonder what in the world can explain dedicating such a large and expensive worship center for only 3 cadets. This is driven by something more than simply equity. It is something powerfully religious that is non-Christian, non-theistic and 'Earth-based' with deep pockets and a lot of political influence."
Erin Roach is assistant editor of Baptist Press.
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