I was just on Montgomery & Co.'s website (the studio that produced Enterprise's opening credits) and was watching the version of Ent's intro that they had posted in their portfolio. The first thing I noticed was the music, it was U2's Beautiful Day 
While the most obvious reason is that they didn't secure the rights to Faith of the Heart, is it possible this was the original song? It certainly fits the date ("Beautiful Day" came out in 2000).
EDIT: Whoops, forgot the link

While the most obvious reason is that they didn't secure the rights to Faith of the Heart, is it possible this was the original song? It certainly fits the date ("Beautiful Day" came out in 2000).
EDIT: Whoops, forgot the link