In Lincoln's day a President's religion was a very private affair. There were no public prayer meetings no attempts to woo the Religious Right. Few of Lincoln's countrymen knew anything at all of his religious beliefs.
It appears to be in the nature of religion itself to be prejudiced against those who are different.
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Basically fundamentalism is a modern phenomenon. In the same way that Hitler evoked a mythological religion of German purity and the glory of the past the Islamists use religion to evoke emotions and passions in people who have been oppressed for a long time in order to reach their purpose.