My entire concern has been about the Bible and Judeo-Christian values disappearing as the primary sources of moral and civic values in America. America has been uniquely good to its citizens (blacks and Indians historically excepted of course, but see below about why America abolished slavery), and this goodness has emanated overwhelmingly from the majority's belief in the Judeo-Christian values they derive from their Bible (the Hebrew Bible and New Testament).
I'm going to do my best to ignore "blacks and Indians historically excepted", as if mass murder and enslavement is some footnote we can just brush aside. Prager goes on to argue that slavery was abolished largely by the effort of those who had religious motivations for their actions. That may well be true, but it ignores the mirror image: slavery was established and maintained by those who quite quickly, readily, and easily offered up biblical justifications (indeed, mandates) for their actions. One can argue that the oppression of Native Americans was nearly exclusively justified via Christian principles (from here on out, I'll continue to use the term "Christian", because I remain utterly confused about what "Judeo-Christian" actually means beyond a token sop to religious pluralism).
Sure, Soviet Russia was viciously anti-Semitic (even with formal rules prohibiting it). On the other hand, so was the historical Catholic Church, and many Protestants--and they didn't even bother pretending to hide it. To act like Christianity--either around the world or in America specifically--has been a wellspring of pure happiness and light is simply delusional.
Prager says he is simply "worried" that, without everyone acknowledging that our rights stem from Christianity, we'll lose the freedoms we hold dear. History does not come close to suggesting that outcome. It does suggest that when we let religious dogma overwhelm our respect for others, and replace the politics of dignity with the politics of division, the lantern of liberty will flicker and die. If Prager is looking at threats to the American way, he can start by looking in the mirror.