Robert Barron argues that the God of the great Christian philosopher isn’t the one the New Atheists try to debunk:
[T]he new atheists hold that God is some being in the world, the maximum instance, if you want, of the category of “being.” But this is precisely what Aquinas and serious thinkers in all of the great theistic traditions hold that God is not. Thomas explicitly states that God is not in any genus, including that most generic genus of all, namely being. He is not one thing or individual — however supreme — among many. Rather, God is, in Aquinas’s pithy Latin phrase, esse ipsum subsistens, the sheer act of being itself.
It might be helpful here to distinguish God from the gods. For the ancient Greeks and Romans, for example, the gods were exalted, immortal, and especially powerful versions of ordinary human beings. They were, if you will, quantitatively but not qualitatively different from regular people. They were impressive denizens of the natural world, but they were not, strictly speaking, supernatural. But God is not a supreme item within the universe or alongside of it; rather, God is the sheer ocean of being from whose fullness the universe in its entirety exists.
It is absolutely right to say that the advance of the modern physical sciences has eliminated the gods. Having explored the depths of the oceans and the tops of the mountains and even the skies that surround the planet, we have not encountered any of these supreme beings. Furthermore, the myriad natural causes, uncovered by physics, chemistry, biology, etc. are more than sufficient to explain any of the phenomena within the natural realm. But the physical sciences, no matter how advanced they might become, can never eliminate God, for God is not a being within the natural order. Instead, he is the reason why there is that nexus of conditioned causes that we call nature — at all.