Bono wrote this song about his father and how, even though they may not have been the closest during his childhood, he still looked up to him and wanted to help him.

He talks about how his father tried to be tough after his mother had died and how he didn't really have to, that he himself could have done something to help.

The prechorus is Bono telling his father that he is there for him, to support him.

The chorus:
And it's you when I look in the mirror-Bono sees aspects of his father inside himself.
And it's you when I don't pick up the phone-Bono regrets not being closer with his father, not calling him as often.
Sometimes you can't make it on your own-telling his father that he can rely on other people sometimes and doesn't have to do everything himself.

The second verse talks about how Bono and his father fought because they were so similar, almost like 'the same soul'. He also says that he knows that if they weren't so similar, they probably could have gotten along better.

The bridge is possibly the most interesting part of the song.
I know that we don't talk. I'm so sick of it all-He wishes that he talked more with his father and that he's sick of NOT talking to him.
Can you hear me when I sing?- He wonders if, in the afterlife, his father can still hear him singing.
You're the reason I sing-Bono telling his father that he is the main cause of his singing, his main inspiration.
You're the reason why the opera's in me-Bono revealed in the 'Go Home: Live at Slane Castle' DVD that his father sang opera. This line is him telling his father that he is the reason music is in him because of the music that he listened to while he was growing up.

Where are we now? I've still got to let you know-Bono wishes that he could have had more time with his father, so he could tell him more or talk to him more
A house doesn't make a home-Bono is saying that home is where the heart is, or something like that, it doesn't matter where they are living
Don't leave me here alone-A plea for his father to come back to him, to not leave him alone in this world, a desperate plea from a child

And it's you when I look in the mirror-again, seeing his father in himself
And it's you that makes it hard to let go-Bono telling his father that it's going to be hard to get over his death, he'll find it hard to let him go on
Sometimes you can't make it on your own
Sometimes you can't make it, best you can do is to fake it-tells of how his father would sometimes make it seem like he was dealing with things when inside he was crumbling
Sometimes you can't make it on your own-telling his father that he could have been there to help him

This is a purely emotional song, written from the core of Bono's being to his father who left this world. This is only my interpretation, even if it's an obvious one, but to me, the way that Bono sings this song and the carefully written lyrics makes this one of the best and most emotional song that U2 have ever made.