My humble opinion...

If you are religeous, you would see REMOVING the words as threatening, as if the government was separating church and state, rather than allowing a connection, and you would want the words kept in....

and - having to say every morning that you DIDN'T believe that your government was under God would be difficult....

and

If you are truly an atheist, you are not afraid of God hearing you say he exists or not, the words themselves should be meaningless, as if the Pledge made you say "One Nation, Under the Easter Bunny"...you may think its silly, but would not feel threatened by the general public's need to affirm this as part of a morning routine.

So - An atheist should not care, and a religeuos person would be threatened.