In Atheism from the Reformation to the Enlightenment, Clarendon Press, Oxford, 1992, David Wootton in a summary of Alan Charles Kor's theories, presents the answer thus (I bolded the relevant parts):

[Kors] shows first of all that theologians insisted that there could be no rational doubt as to God's existence: the Bible, after all, said 'the fool has said in his heart "There is no God."' No sensible person could reach this conclusion using his reason. Yet, because Aristotelian philosophy insisted that objections to every line of argument must be explored, theologians did not heistate to propound arguments against the standard demonstrations of God's existence. The 'atheist' was thus primarily an invention of orthodox theology: a critical interlocutor, whose task it was to test orthodox reasoning and press for its improvement.

Further on (p. 25) Wootton explains the use of the term 'atheism'. The term itself only came into use in the sixteenth century. The word stems from ancient greek, but it was not used in the Middle Ages:

This is not because there was no unbelief in the Middle Ages. Around 1020, for example, two clergymen in Orléans apparently insisted that the universe had existed from eternity, that heaven and hell were fictions, and that the doctrine of the Trinity was incoherent. This, in the eyes of contemporaries, was impiety, not atheism.

So the basic answer is that the philosophical proof of the existence of God was used in a traditional aristotelian sense, purely as a theoretical excercise. But not because there wasn't any unbelievers at the time, though.

Edit: I should perhaps mention that Wootton disagrees with Kors' (and originally Lucien Febvres) claim that atheism continued as an invention of orthodox Christians throughout the 16th and 17th centuries. It is not really relevant for the question at hand, but it needs to be pointed out, so as Wootton does not seem to be misrepresented by myself in this post.

I'll add that it's also possible to see Aquinas' proofs of God's existence as playing a key role in his overall project to integrate Aristotelian thinking into Christian theology. If Aquinas is asking other theologians to reject traditional ideas in Christian theology, he needs to demonstrate that the ideas he's asking them to reject are not crucial. He does this by giving proofs of God's existence that don't rely on the old ideas, and instead rely on the new ideas.

It was also the case that Aquinas firmly believed that reason and faith went hand in hand. To him, it was important to demonstrate the connections between his Aristotelian worldview and his faith in God. Offering Aristotelian proofs for God's existence was a way of demonstrating the way that reason and faith support each other, and it in particular showed the way that Aristotelian reasoning supports his faith.

It's true that virtually everyone believed in God at that time, but knowing the reasons for what one believes leads to greater understanding. If we don't know the reasons for what we believe, we remain at the level of mere opinion. As you can see from the questions that Thomas considers before his proofs for God, some claimed that God's existence was obvious (i.e. immediately known to all without need for any proof), while others claimed that no proof was possible but that God's existence could only be taken on faith. Thomas's position is that the existence of an intelligent creator of the universe, while not obvious, can be known through philosophical reasoning, based on what we observe about causality. (St. Paul confirms this in Romans 1:19ff.) He retools arguments from the ancient philosophers to do this, and argues that some attempts to prove God's existence, like St. Anselm's, were unsuccessful.

However, as Thomas goes on to explain, this kind of reasoning does does not prove everything that Christians believe about God. That God is a Trinity, and that Jesus is the Son of God, for example, are truths that Christians take on faith, believing that God has revealed them to us. Hope this helps.