From the article:
“The VA’s actions undermine our Constitution, which intentionally establishes a secular government in order to preserve religious freedom, a right enjoyed by individuals,” Sam Grover, associate counsel for the Freedom From Religion Foundation, wrote in a letter to Wilkie objecting to the standards.
At the VA hospital I attend, the campus consists of something like 40 buildings and hundreds of thousands of square feet of floor space. Out of all that, there are two chapels on the campus, one on the third floor of Building 2 and one on the fourth floor of Building 2. The larger of them is maybe 20 feet x 30 feet, the smaller is probably about 12 feet x 15 feet. I was in the larger one just a couple of weeks ago -- I spend a few minutes in one or the other pretty much every time I'm at the hospital. There was some Roman Catholic literature in a rack near the door, but no Bibles, no hymnals, no Qurans, and nothing at all Hebrew in nature. There is an altar in each chapel, but I don't recall whether or not there is a cross on either altar. (I'll try to remember to pay attention the next time I'm there.)
Chapels, and chaplains, in government facilities have to serve a "clientele" that comes from a broad spectrum of religious backgrounds. Since the entire purpose of a chapel is worship, it should stand to reason that a chapel should provide whatever is required to support worship. In a VA hospital, a chapel might be called upon to house a Roman Catholic mass, a Protestant Christian service, a Jewish service, a Muslim service, and possibly a service or ceremony for/by some other religion ... all in the same chapel facility, and possibly even all in the same day.
IMHO, VA chapels should certainly allow, if not provide, the basics of what's needed for conducting services for the mainstream religions. That might get confusing -- for example, the Roman Catholic Bible is different from any of the Protestant Bibles. But ... pick one. The major books of the New Testament are in both. Not everyone needs to hold a Bible in their hands during a mass or a service, so have a few in a box or on a shelf near the door for those that need them. Same with the Quran. If a particular city or region has a high percentage of adherents of some other religion among its veterans and they want their religion to be represented in the chapel, their literature should be allowed in, and clergy from their religion should be allowed to conduct services in the VA chapel.
Freedom "of" religion doesn't mean freedom "from" religion. If atheists don't want to worship God or be troubled by seeing Bibles, they don't have to set foot in the chapel.