The White House recently addressed a similar petition, and the response was inadequate. There is no role for religion in the public square; any good that can come from religion, can come without it.
The phrases were added to our pledge and paper currency during the height of the Red Scare, and were directly attributed to Christianity to infuse patriotism - this is a direct violation of the first amendment. The United States has acknowledged atheism as a religion, and these phrases violate the first amendment rights of many.
This is a violation of the Establishment Clause. Remove these phrases, as they are unconstitutional. We are not asking for the President's opinion about religion, as it isn't important, but that he abides by the Constitution.