Get down on your knees and pay your dues
I said this, and my mom freaked out, thinking it was a weird sexual reference. I have never heard it that way, and teachers at my school say it frequently.
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That's the price you pay, Lord, there ain't no other way
But to get down on your knees and pay your dues
You're asking about a music lyric, but at least this time about a specific one. And you're asking about one which seems to provide a straightforward interpretation. Namely that
to get down on your knees
means to pray.
It is unclear whether and pay your dues refers to something you do while you are on your knees (praying) or to a totally different action.
The reason the phrase about get down on your knees is relatively unambiguous is because there are other religious elements in the song, such as the invocation of the Lord in the line previous to the one you ask about; and the song's title Cross to bear, which has come to mean for some religious people almost a definition of life, at least regarding the sufferings that "God sends their way". Also, to walk in darkness has possible religious references (see Psalm 23 or the Christian classic Dark night of the soul).
So unless there is some highly esoteric meaning hidden in these pretty straightforward lyrics, I'd take the obvious meaning to be the meaning intended. Not every song contains deep mysteries.
One explanation of the songs of Billy Joel says:
The clichéd lyrics include phrases such as “get down on your knees and pay your dues” and “we all have our cross to bear". To the one who he addresses the song Joel is saying he has to go out on the road for his career or his "freedom," and she will just have to learn to live with that reality.
(Page 91,The words and music of Billy Joel).
But of course that is just the author of this book's interpretation.
Finally of course, somebody can always lift a song lyric from its context and use it a completely different way than it is presumably used in the song.