One of the reasons that the Enlightenment was so hostile to a lot of Aristotelian theory, was that Aristotle opposed atomism and materialism. This offended the secular-'humanists' [Atheists], who demanded in various theorems that the material world, as identified by rationalist [positivism, where the mind is the only reality]; could explain everything. There was no need for many of these 'Enlightened' thinkers for a God, supernaturality, miracles or 'complexity'. Nature or its material dialecticism could explain everything.
There is of course plenty wrong about much of what Aristotle said. However, he was strongly and correctly in my view, of the opinion that reason itself had many issues and a definable limit. For example is the 'rationalism' of Epicurus [materialism] from the 4th century BC, reconcilable with the 'rationalism' of say Pythagoras [everything is mathematical], Democritus [everything is chaotic atomism]; Marxism [history is great sweeping materialistic phases]; or Atheism [reason is a by product of chance and chaos] ? Aristotle knew that rational theologies were not only corrupt, often-times weak in their logic, but open to divisive debate and censure.
As Wiker states, 'Nominalism' [from the Latin word to name] is a rationalist theology which believes that nothing is real. Nominalists conclude that the name cat is artificially affixed to a creature with a cell agglomeration which is in the shape of what our mind calls a cat. But that name is not real, neither really is the cat. It is just a lump of atoms. This 'relativity' is often embraced by the great and good as the highest form of 'rationalism'. It is nothing new. Nominalism was around in 300 BC and rejected by Aristotle. Cats are distinct creatures, and are not dogs. If you can't make that distinction you are simply a lunatic.
The Church therefore sided with Aristotle during the Middle Ages starting in the 4th century to stand against atomism, materialism which by their own logic, preclude the spiritual, a soul, the Eucharist and the entire canon of Church belief. Wiker makes this important point and this is the key reason why 'Enlightenment' 'thinkers', are so hostile to Aristotle and so contemptuous of Medieval Church Scholasticism. They desire to eradicate Church canonical liturgy and replace it with atomistic materialism as espoused by Epicurus who was in vogue in the 17th and 18th centuries and Atheist-Darwinism which builds on Epicurus' ideas and demands that you believe nothing created everything by magical processes of naturalism.