Respect for All Beliefs, or Just Religious Ones?

The Washington Times reports that the Naval Academy will retain its noonday prayer described thus:

" The brigade of about 4,000 students gathers at noon at King Hall. They stand by their chairs for announcements and the welcoming of any guests. Then, one of the school's six chaplains delivers a nondenominational prayer. Sometimes a moment of silence is observed instead.
'Those who want to participate may do so,' Cmdr. Gibbons said. 'Those who do not wish to participate do not have to pray. But they are expected to remain respectful for those who do.' "

While the ACLU might have a problem with this, I don't, except. (There's always an "except".) A paper, maybe the Times, did a piece recently on the chaplain problem in the military, including a table listing the number of military personnel by religious affiliation and the number of chaplains. The focus was on evangelical chaplains, but I was fascinated to see that around 100,000 military had no affiliation. Of course, there were no chaplains with "no affiliation".

My point is that there seems to be no military context/ceremony that would call for religious people to "remain respectful" for those who have different beliefs.