This poem is part of the Amoretti cycle of sonnets, which Edmund Spenser wrote to record his courtship with his beloved (and eventual wife) Elizabeth Boyle. The speaker in the sonnet cycle (and perhaps Spenser himself) did not have an easy time winning the heart of his lady, however, as Sonnet 48 reveals.
Apparently, the speaker has sent his beloved a letter declaring his love for her, but it does not go over well. In fact, the lady burns the letter. The speaker, using the poetic technique of apostrophe, speaks directly to the "Innocent paper" burned by his beloved's "cruell hand." She takes her "yre," her anger, out on the poor paper that couldn't help but express the cause of its master, and she sacrificed it to the "greedy fyre" that turned it into ashes. The metaphors here are delightful.
The paper deserved better than that, the speaker continues. Burning is the punishment of heretics (and in Spenser's day, it really was; those who failed to conform to religious orthodoxy sometimes did find themselves burned at the stake), and there is nothing heretical or treasonous about what the poor, innocent paper contained. It was merely a painful plea of a grieving heart, for the speaker's beloved refuses to love him in return.
What's more, the lady does not care about the speaker's grief. He has poured forth the "anguish of his hart" to her in his letter, for she will not hear him in person. He feels like he is near death because of his sorrow and pain at her refusal. Yet he can take comfort in one thing; even though the paper is burned, his words will remain. There is power in words, and his beloved probably read the letter before she burned it. Therefore, the words have entered her mind, and they will continue to speak to her in her memory, whether she likes it or not.