For some reason, I see this as another one of those u2 songs that mean a whole bunch of different things. I see it as a dedication to NY after 9/11, but I see it also with some references to Ali.
"Oh, you look so beautiful tonight" obviously, but in the second verse it sounds like he's talking to Ali.
"I've seen you walk unafraid, I've seen you in the clothes you made. Can you see the beauty inside of me? What happened to the beauty I had inside of me?"
I say this because it fits and a little while back Bono talked in detail about his love for Ali in a Vanity Fair article and mentioned how she used to make her own clothes.