You might also try "Is Energy conserved in General Relativity",
http://math.ucr.edu/home/baez/physics/Relativity/GR/energy_gr.html.
That's not as good a source as Caroll's textbooks, but it is probably about as good a source as the "preposterous universe" link. Both are written by persons knowledgeable in the field, but both are popularizations with the associated pitfalls.
The basic issue, though, is that an "expanding universe" is not a Newtonian concept, but a concept in General Relativity. So Newtonian theory is not enough to tackle this issue, if all you have is Newtonian theory, you'll wind up somewhere between slightly confused and very confsued. And General Realtivity is basically a graduate level topic - there are some undergraduate level introductiory treatments, but typically a discusssion of energy is not included in introductory treatments.
At the lay level, the most accurate statements tend to be very vague. For instance, from the FAQ I cited:
Is energy conserved in General Realtivity?
In special cases, yes. In general, it depends on what you mean by "energy", and what you mean by "conserved".
The more detailed exposition explains this a bit further, but it may be hard to follow without the right background, and is still rather general.
In flat spacetime (the backdrop for special relativity), you can phrase energy conservation in two ways: as a differential equation, or as an equation involving integrals (gory details below). The two formulations are mathematically equivalent. But when you try to generalize this to curved spacetimes (the arena for general relativity), this equivalence breaks down. The differential form extends with nary a hiccup; not so the integral form.
The preposterous universe article takes a different course:
At first glance this seems to disagree with Baez's article, but they're both simplificaitons/popularizations of the same, complex, theory. The point behind Caroll's statement is that in the most general case, we do not have a conserved notion of energy in General relativity. Historically, this was noticed early on by Hilbert. In another tidbit, rather than tackling the issue himself, Hilbert gave the problem to his assoicaite, Emily Noether, and this resulted in Noether's theorem, which relates symmetries to conservation laws.