In a fairly bluntly worded official Air Force article, SSgt Shelton Sherrill provided a decent explanation for the sometimes misunderstood role of a military chaplain:

According to the first amendment of the Constitution of the United States, Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof. For military members, chaplains are one of main advocates to help them protect this right.

Chaplains…provide religious accommodations to ensure everyone is free to exercise their beliefs, provide ethical advice to leadership, unit visitations and confidential counseling.

Edit: Actually, commanders are the ones who provide religious accommodations, not chaplains, as chaplains have no authority to authorize anything. (Chaplains famously have “rank without command.”) However, Read more