I always heard the term referring to military chaplains. But I was watching an episode of Death Valley Days and a guy called the new reverend in Carson City a Sky Pilot. I wondered why they would use a modern term like that.
But a little research revealed the first use was around 1865 and again in 1883 and refers of the a pilot in the nautical guide sense. Guiding souls to heaven.
Ya larn something new every day.