If an atheist says that he does not believe in God because he does not see any evidence of his existence, then there is a sense in which we can agree with him. If the best evidence for a stone's existence is the actual stone lying on the ground for all to see, no theist or scientist will ever be able to provide such evidence for the existence of God.
It is a good thing, then, that Aquinas does not offer any arguments of this type in order to prove God's existence. In fact, his method is quite congenial to a modern audience since he always begins with what his eyes, ears, nose, mouth, and hands tell him. It is perhaps easy to be fooled when reading proofs for God's existence and descriptions of His nature; how could these lofty things possibly be concluded from examples like hands holding sticks pushing rocks!?
Aquinas' reasoning is a movement that begins with effects and progresses towards what is ultimately a first cause. Notice, God is first known as a cause. It is through the relations that God has with his creations that we know He exists. Now this is the crucial point: It is what we know about the material world that necessitates God's existence. The theist does not see anything the atheist does not, they both touch, see, smell, hear, and taste the same reality.
The central difference, then, between the atheist and the theist is not what each has to say about God; it is what they have to say about the stone lying on the floor, or the hand holding the stick pushing the rock. And what they say, exactly, will depend upon their modes of consideration. The atheist refuses to consider the objects in the material world in a way that the theist does not. It does not matter whether you call this mode of consideration metaphysics, ontology, or first philosophy. What matters is that the atheist qua atheist is positively limiting the use of his reason and so cannot see what makes God absolutely necessary to a coherent image of reality.
Aquinas is more scientific than Richard Dawkins.