In "A Hymn to God the Father," the speaker grapples with one of the oldest difficulties of religious faith: it's hard to believe that God is truly all-merciful and all-loving.
Reaching out to God in a direct and desperate apostrophe, the speaker wonders how God could possibly forgive him for his many sins. The speaker, this question implies, would certainly find it hard to forgive himself, were he in God's place.
That's partly because, from this speaker's Christian perspective, everyone has sin in them from the very day they're born:
Wilt thou forgive that sin where I begun,
Which was my sin, though it were done before?
Here, the speaker alludes to the doctrine of original sin: the Christian idea that people are born sinful and need to be washed clean by baptism. This sin, the idea goes, was indeed inherited from "before," all the way back when Adam and Eve ate the fateful forbidden fruit. Christ's self-sacrifice redeems that sin, but it's still there.
This is a reverent theological question to start with; the speaker is essentially saying, God, do you really have it in you to forgive me for the sin I was born with, as my faith says you do? The next question, though, gets uncomfortably personal:
Wilt thou forgive that sin, through which I run,
And do run still, though still I do deplore?
The sin the speaker's talking about here isn't just the sinfulness inherent in human nature. It's all the sin he's committed himself and keeps on committing, even though he "deplore[s]" (or despises) it. His diacope on "through which I run, / And do run still" evokes his pain: alarmed by how he just keeps doing things he doesn't want to do, he seems exhausted, discouraged, and frightened.
Notice, too, the way the speaker uses anaphora in these lines. Starting both of his questions with the words "Wilt thou forgive that sin," he sounds as if he's making a formal prayer, getting down on his knees to ask God: Truly? Can you really forgive me for all this? This poem will become not just a hymn, but a confession and a prayer.