Excellent question. I worked in politics after the military and when I was in the West Wing during the Bush admin it came up once! They said the same thing, that it was the ship's idea. I reminded them that aircraft carriers don't have printing presses so it would be a little hard for the sailors to put that kind of banner together.
It could be that the ship's leadership wanted something like that (they are politicians too). But at least in my squadron we were all furious the president was coming because we had been out at sea for the longest nuclear and F-14 cruise of all time (10 months) and we just wanted to go home to our families but now we are delayed another week for a political stunt and have to spend the next two weeks cleaning the ship in preparation.