Linnaeus was from the generation of naturalists who spent their life cataloging and describing life forms, which was a time consuming pursuit. It was obvious to lump animals into groups based on physical similarities. Man looks much like an ape and chimpanzees are smaller apes, and so on. None of this challenged Holy Scripture.
The problem Darwin caused for the religious of his day, was not so much that man descended from some ape-like creature, but that the time span required for this process, was totally contrary to the creation story from Genesis. This was occurring at the same time that geologists were recognizing that many visible natural structures, which had been attributed to the flood of Genesis, could not be explained by the erosion effects of a 40 day flood. Darwin's work came at a time when Natural History as interpreted through Scripture was being challenged on all fronts. The religionists had already conceded to astronomy and Natural Selection as an engine of creation was seen as an even greater threat to the validity of Scripture as an explanation of the natural world.