The United States government has a long history of preferring Christians over those of other religious backgrounds, even though it was clearly not founded upon Christianity. The Constitution does not mention Christianity, and the Treaty of Tripoli (1797) very clearly states that "the Government of the United States of America is not, in any sense, founded on the Christian religion" in article 11.
Yes, the majority of United States citizens are Christians, but one thing about the United States that makes it great is that it hears the voice of the minority.
The administration, to further the separation of church and state, should remove "In God We Trust" from the currency and "under God" from the pledge. These phrases alienate those citizens who do not believe in the Judeo-Christian god.