Atheists becoming less unpopular?

[Neo-Scholastic]

I don't think you are reading that correctly. Aquinas is most definitely not saying that human rights come from earthly rulers. Notice how he referes to "true good" and "divine justice" and how someone can be good with respect to the ruler but still in opposition to Divine justice. Human rights are grounded not in the ruler's whim but in the Divine good to the extent that it comes through the ruler.

I don't see "Liberty & Justice for All" in Aquinas' teachings.  In fact, Saint Thomas was quite content with the institution of slavery:

Considered absolutely, the fact that this particular man should be a slave rather than another man, is based, not on natural reason, but on some resultant utility, in that it is useful to this man to be ruled by a wiser man, and to the latter to be helped by the former, as the Philosopher states (Polit. i, 2). Wherefore slavery which belongs to the right of nations is natural in the second way, but not in the first. (Summa Theologica II II, 57, 3, ad 2)

http://www.newadvent.org/summa/3057.htm

And, so, morality, and hence, the "natural law" evolves over time, something that one would expect under naturalism but not under super-naturalism.

You seem to be deliberately misreading Aquinas. Look back to Article 1 of the same Question and you will find this:

"I answer that, It is proper to justice, as compared with the other virtues, to direct man in his relations with others: because it denotes a kind of equality, as its very name implies; indeed we are wont to say that things are adjusted when they are made equal, for equality is in reference of one thing to some other."

And in the part you quoted Aquinas is answering these objections:

"Objection 1. It would seem that the right of nations is the same as the natural right. For all men do not agree save in that which is natural to them. Now all men agree in the right of nations; since the jurist [Ulpian: Digest. i, 1; De Just. et Jure i] "the right of nations is that which is in use among all nations." Therefore the right of nations is the natural right.

Objection 2. Further, slavery among men is natural, for some are naturally slaves according to the Philosopher (Polit. i, 2). Now "slavery belongs to the right of nations," as Isidore states (Etym. v, 4). Therefore the right of nations is a natural right.

Objection 3. Further, right as stated above (Article 2) is divided into natural and positive. Now the right of nations is not a positive right, since all nations never agreed to decree anything by common agreement. Therefore the right of nations is a natural right."

It would be very odd for Aquinas to reply to these objections by agreeing with them, which is what you are suggesting.