There are Chaplains from many of the different protestant denominations. The Seminary I am currently attending has a degree track specific to chaplaincy in the military. What the military requires is a seminary degree around 60-70 hours (not quite an MDiv but a MDiv would certainly be advantageous) plus licensure and ordination in a recognized denomination. There have been BBFI Chaplains, IFCA Chaplains, Christian and Missionary Alliance Chaplains, and so forth.
What stinks is that with "Protestant" you have a broad road which may include Episcopalian, Lutheran, Seventh Day Adventist, and possibly even Mormon! You just do not know what you are getting when you ask for a "Protestant" Chaplain!