http://www.catholicculture.org/news/headlines/index.cfm?storyid=3425"And now I am no more in the world, but these are in the world, and I come to thee. Holy Father, keep through thine own name those whom thou hast given me, that they may be one, as we are" (John 17:11).
I don't think any person in their official capacity as an employee or officer of government in the U.S. calling the pope "Holy Father." Doing so in essence is calling the pope God on earth.
We have separation of church and state in the U.S. Our government should therefore not endorse Rome's claims that the pope is the representative of God on earth, and that the titles of God can now be applied to the pope.
But I doubt Obama is the first president to cross the line on this one.