As an atheist and a former military member, that would be pretty irritating.
Religion provides a competitive advantage during combat, and should be supported even if you're not religious yourself. It's a fighting advantage we have over the Chinese and Russians. Most human specific traits can be traced to their competitive advantage during tribal warfare. Large brains, religion, speech, walking upright to carry weapons, having well-lubricated armpits that respond to stress, all were selected for on the battlefield. Based on archaeological evidence of religious items, the first tribe that discovered religion wiped out all the other competition. If atheist soldiers want to survive combat and be on the winning side, they should just suck it up and go along with the program as best they can.
I have a question. I know that atheists deny the reality of God. Do they also deny the reality of the human soul?
Another question: What is it about God that gets atheists so upset?
Still another question: Are atheists generally unaware that the DoI and the Constitution which instantiates its values speaks of "Nature's God," the Creator? That the entire American idea of liberty is predicated on the understanding that God gives human beings their natural rights, not governments; and that such rights are unalienable because they are divine endowments?
Having spent a number of years as a chaplain in the US Army, one must understand the LEGAL and CONSTITUTIONAL place of chaplains in the military to understand this program and why it is no problem.
1. The courts have upheld the place of religious leaders (chaplains) in the military. The reason for this is that the US Constitution guarantees religious freedom AND religious exercise to every citizen. One must understand that religious freedom does not mean "I can pray or talk religion when I want to." It means you can FULLY practice all aspects of your religious faith. In short, to FULLY practice one's religion one must have that religion's FULLY authorized religious ministers/priests/rabbis available in order to do so. This is not about "10 commandments in front of town hall." That would be the topic of "preferential treatment in a government setting." The military chaplaincy is about "American citizens having their right of free exercise removed."
2. Therefore, given the appropriate presence of military chaplains, it is long acknowledged by military commanders that these highly trained officers in their midst have unique skills in areas such as counseling, family programming, morals education, law of war and just war, AND morale and esprit de corps assessment, and etc.
3. They, therefore, have a two dimensional task in the military: (1) religious leader (2) troop support. One is religious and one is not religious. On the "religious leaders" side, they cannot be part of a commander's "mandatory" attendance programs. On the "troop support" side, the commander can certainly require the attendance of troops. (For example, the battalion chaplain is typically the officer chosen to provide "suicide prevention" briefings to all troops. These are mandatory attendance briefings.)
4. "Esprit de Corps" (Spirit of the Unit) is an ancient concern of military commanders in that it is closely aligned with "morale." The morale of a unit is that sense of team unity that is radically energized to mission achievement and cohesiveness.
5. One cannot speak of "Esprit de Corps" without speaking of the "esprit" of the member. The "spirit" of the member, therefore, has to do with the morale of the member, with their "essential core" and its energy.
6. The "morale" of a unit is not a passing concern of a commander. It is one item on a checklist of battlefield preparedness that is a requirement, and one item on which this commander's fitness report will be based.
7. While the chaplain is certainly not the only member of the commander's staff whose mission touches on morale, he is one staff member who is trained is assessing the "core" of the individual and of the group. Like the commander, he visits among all the troops, speaks to many of them, and has eyes and boots on the ground in the midst of their circumstances. If they're down, he can see it. If they're up, he sees that, too. None of this, mind you, necessarily has anything at all to do with the religious side of his mission. Some of those he sees will, of course, be a part of the religious community in that unit, but many will not be. If the chaplain sees a depressed soldier, he doesn't ignore them if they have no religious affiliation.
Instead, he tries to help that soldier through a tough spot. Most times that wouldn't involve any religious discussion at all. He'd say something like, "Private Snuffy, what's going on, man?" Pvt Snuff might respond, "Wife back home is having trouble." "What kind of trouble, Snuff?" "Well, she made a mistake in paying bills and they're broke." "Snuff, why don't we get in touch with the family support group back in the states and have them contact her. They have all kinds of help resources. What do you think?" "That'd be great, Chappy." "Good...give me her name and number. I'll pass it on and set something up."
That, my friends, is a "spiritual (morale) assessment" and a follow-on response.
The freedom from religion foundation doesn't know didly about the job of the US Military Chaplain.
And that's what really should be taken away from this article.