Lyric discussion by kensredemption 

Cover art for Fix You lyrics by Offspring, The

Hmm...from the looks of it, as well as hearing it, it seems like this is a relationship that's falling apart.

The girl's not who she used to be, since she's fallen from grace, hence: The "Broken Wing" and the "Empty Glass" which could have contained liquor at one point.

She points out how "We'd all like to re-arrange" leading the listener to believe that their relationship isn't picture perfect.

The guy notices the changes in her, and tries to "fix" her - Put her back the way she used to be, or "How (he) wants (her)".

He's hurting inside because he can't figure out what's wrong or how to fix what problems they have in their relationship.

He notices that she sees something romantic like the stars as nothing more than "Holes in the sky". And the fact that God's tears are for her, is because she can't see the sentimental value in them, as well as her boyfriend/fiancee/etc.

I'm assuming the reason "(He's) in her rain" is because he feels like he doesn't mean much more than a passing rainstorm.

In the end though, he remembers that even though they'd like to re-arrange, there's not much he can do.

In any case, as I've posted along with my other comments, this is just my opinion. I don't expect you to take me seriously, but I'd like it if you didn't flame me for saying what I've interpreted the song to be. If I offended you in someway, I give you my apologies in advance.