It is certainly possible to present evidence for both sides of this issue today.
To argue that Hughes and Prothero are/were wrong, we can look at issues surrounding Muslims in the US today. We can see the uproar over mosques being built in the US. This happens when they are built in sensitive places such as a few blocks from "Ground Zero" but also when they are built in places that have no such history. There is also a great deal of hatred of President Obama from those who believe that he is secretly Muslim. These are certainly signs that America is not living up "to what it claims to be."
On the other hand, we can look at increased acceptance of Christian sects that were once distrusted and discriminated against. We need look no farther than the Republican primaries for this. Two of the men still in contention (if we use the term generously) for the nomination are Roman Catholics. The man who will almost surely be nominated is Mormon. The fact that this is not an issue to most of the American populace shows that we are progressing towards what we claim to be.