Technically the war on RELIGION is NOT one on Christianity because the name of Christ never gets used. The god they are referring to is Baal.
"In God We Trust" and "under God" in the pledge came later, too. Those phrases were adopted in the 1950s and were all about showing that America was a Christian nation in the face of godless communism. They don't go back to the founding fathers, who only had "e pluribus unum" as our motto.
Now I suppose our enemies are the Muslims who worship the same God as Christians, but meh...religious fighting has never interested me much.