Yeah your experience does not seem as bad! Now they have the prayer breakfast and "spiritual fitness" etc! When I filed a complaint against that chaplain, I called IG and they basically told me to just deal with it! They said there are mandatory spiritual briefings and stuff like that! I told him that if I wanted to hear that I would go to church! But I do not know where to draw the line in the sand with these folks! I am almost out of there but I look out for the young soldiers also! I felt like the minority throughout most of my career! It should not be that way in an environment that they say is so professional!
I bet it's apathy above all. They might not even be agnostic. Religion just wasn't crossing their minds when reception was asking them for their religion.
That being said, I became friends with 2 other atheists and 3 agnostic~atheists my age at boot camp.
It was only after boot camp that I researched about atheists in America and I realized I was pretty lucky to have been around those guys.