Like many of Shakespeare's sonnets, this poem is an expression of love. In order to express your love, you have to talk about it, define it, examine it. In telling his mistress that he loves her, our speaker also has to give us an idea about what his love is like. This poem is partly about where love comes from, what motivates our feelings of affection for someone else. Specifically, it's about finding love in spite of (or maybe even because of) physical flaws.
The speaker of this poem keeps his reasons for loving this woman to himself. He makes it clear that her appearance isn't crucial, but most of his positive feelings about her remain a mystery.
This poem reveals an ambiguous kind of love, one that seems heartfelt and sincere, but also tinged with a kind of harsh anger. The conflict between these two feelings is never fully resolved.