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This has been a problem for a while - a distressingly large number of people in ranking positions in the military treat the US military like it's a branch of their religion. They know there are laws against what they are doing ,which is why the are careful to walk the line right on the edge of legality following the letter of the law but not the 'spirit' of the law. One example is sergeants training cadets and using their position of authority to "strongly encourage but not quite order" the cadets to behave religiously. (For example, "I can't order you to go to church, but if I see you missing from church again I'll see to it that you get assigned the worst jobs.")
I do believe some high ranking military officials have a tendency to influence their service members to become familiar with a specific faith. However, I also believe that these leaders do this is because they want to provide a different approach to teach, coach, and mentor their troops. Perhaps some leaders refer to their particular religion when "counseling" troops because they relate to them from a time when they were in need of some direction themselves and becoming loyal to a faith is what helped them the most. I agree Mr. Weinstein stating that, "the Chaplins are the least of their problems." I have never been influenced to convert my personal faith by a military Chaplin. I have always found military Chaplins to be non-biased spiritual counselors and have observed many troops, including myself, to be very receptive to the services they provide.