Gene Callahan has an excellent post on how modernity creates problems for correct historical interpretation. Another good example of this is Gibbon’s commentary on Christianity in The Decline and Fall of the Roman Empire, as Lance Ralston points out on his “History of the Christian Church” podcast.
The biggest problem – which Gene does an excellent job of extracting in his post – is the assumption that any experience of or with the supernatural must be interpreted as to have a physical, chemical, psychological/psychoneurotic cause. By doing so, the modernist can confirm his belief that such levels of reality do not exist. But as Chesterton points out, the Christian does not deny scientific reality (as some say we do); we simply believe there is more than scientific reality.