1) make it
a) to reach a goal, to succeed in doing something, to be able to be present at a particular event
b) To have sex, in 80's slang.
2) make it through (obj.).
to survive through a difficult period, illness or accident.
You have to keep in mind that this is a song, that song-writers very often do not choose words or phrase a sentence for grammatical correctness. The aim is to rhyme, or to emphasize something.
In this case I believe the sentence should beg the question ("make it through what?").
Perhaps Faith Hill can answer that. Or use your imagination.
You will note though that "through" rhymes with the following sentence ending "you".