Aquinas separated nature from grace in theology. The spiritual world and the earthly world became separated. The earthly world became what was "real" and the spiritual world was the "hypothetical."The largest problem with this is that it's just plain nonsense. St. Thomas said nothing of the sort, and I can't conceive of any way that what he did say could rationally be construed like this. In the first place, he was an orthodox Christian, and to separate nature from grace smacks of Pelagianism. Secondly, it's irrational: God created us freely and without compulsion; hence creation was an act of grace from start to finish.
Thirdly, it seems that Schaeffer never bothered to read as far as the sixth article of the first question of the Summa Theologica. Because if he had, he would have realized that his construal of Aquinas was wrong.
The principles of other sciences either are evident and cannot be proved, or are proved by natural reason through some other science. But the knowledge proper to this science [theology] comes through revelation and not through natural reason. Therefore it has no concern to prove the principles of other sciences, but only to judge of them. Whatsoever is found in other sciences contrary to any truth of this science must be condemned as false: "Destroying counsels and every height that exalteth itself against the knowledge of God" (2 Corinthians 10:4-5) (ST I Q1 A6 ad 2).St. Thomas says here that because the knowledge that is the subject of theology comes by revelation from God, it is consequently superior to the other sciences in the sense (among other ways that it is superior) that it is more certain. We attain to knowledge in the other sciences only with great difficulty: we may make errors of reason, so that we reach incorrect conclusions; on the other hand, we may draw valid inferences that are nevertheless false because the evidence we have at hand is inadequate. But revelation suffers from neither of these defects, and because it comes from God it cannot possibly be false because God does not lie, and his knowledge is perfect. This being the case, it rightly serves as the standard by which all the other sciences must be judged: so that, as he says, "Whatsoever is found in other sciences contrary to any truth of this science must be condemned as false." This being the case, it seems to me to be silly to say (as Schaeffer did) that Aquinas separated grace from nature. Nature is subject to judgment by revelation, as the saint says here.
Nevertheless, it must still be said that St. Thomas affirmed that reason can arrive at truth, and that it is not dependent upon theology to do so. To be sure, it is limited as to the scope and extent of the truth it can discover. Reason cannot discover those things that can only be known by faith, such as the fact that God is triune. It seems ridiculous to say that this affirmation of reason's (limited) power to discover truth in any way divorces nature and grace. To the contrary: what this means is that God has created us in such a way that we are well-suited for life in the world. Our senses and our minds reliably allow us to understand creation.
Far from being "hypothetical," one would be closer to the truth if he said that Aquinas considered the spiritual world to be more real than the physical world. To assert the contrary about him is either grossly ignorant or downright slanderous. Modern philosophy started with Descartes' rationalism, not with St. Thomas.