How we cite our quotes:
And trouble deaf heav'n with my bootless cries, (3)
This line says so much about the speaker's state of spiritual despair and his attitude toward a God that doesn't seem to care about his problems. Our speaker feels that his cries to God are useless ("bootless") because "heav'n" has turned a "deaf" ear on him. Like we've pointed out elsewhere, our speaker seems so bitter and so isolated from God that he can't even bring himself to say the name "God."
Haply I think on thee, and then my state,
Like to the lark at break of day arising
From sullen earth, sings hymns at heaven's gate; (9-12)
When we reach these lines, the speaker has a dramatic change of heart. Instead of feeling like "heav'n" is "deaf" like it was back at line 3, our guy says that he feels like a bird that rises up and "sings hymns at heaven's gates." Does that mean the speaker has changed his mind about God and is now praising heaven? Is God listening this time? If so, what's changed? Has heaven cleaned the wax out of its ears or something? Not necessarily. What's changed is that the speaker suddenly remembers an important person in his life ("thee") who makes him incredibly happy.
For thy sweet love rememb'red such wealth brings,
That then I scorn to change my state with kings. (13-14)
In the final couplet, our speaker insists that it's the "sweet love" of another human being ("thee") that's brought about a spiritual rebirth in him. Come to think of it, this reminds us of how Romeo and Juliet and are always running around comparing their love (a.k.a. their steamy teen romance) to a religious experience. By the way, this whole "love as religious worship" stuff is a pretty common metaphor in sixteenth-century literature and poetry. It doesn't necessarily mean the speaker is romantically or sexually involved with "thee."