I understand your confusion with this sonnet, and Shakespearean sonnets in general. The beauty often lies in the complexity, which makes them so great once you've figured them out. In the meantime, they can definitely be tricky.
Sonnet 130 is one such sonnet. Here, Shakespeare is actually using some common imagery from his time to do two things. First, he is describing the beauty of this "mistress." Second, he is making fun of all other poets and poetry by taking several cliche images and showing--ironically--that this mistress' beauty surpasses all of these natural elements. In fact, based on the ironic nature of this sonnet alone, I think perhaps Shakespeare would be a little offended by the cliche comparison of this piece to the "don't judge a book by its cover" theme.
Nevertheless, the comparison is there. The sonnet opens with
My mistress' eyes are nothing like the sun.
This image is then built on with further images of comparison, each growing slightly more brazen ("breath that from my mistress reaks" and "music hath a far more pleasing sound" than her voice). On first reading, it sounds like the speaker here doesn't think much of his mistress at all. She first appears to be ugly, stinky, and noisy.
And yet, by heaven, I think my love as rare
As any she belied with false compare.
The speaker finishes by giving an even higher tribute to the mistress than if he had simply compared her to roses and music and coral. The real message is to every other romantic poet, accused here of making "false" comparisons for the women in their poetry. This sonnet says, basically, I have such a wonderfully rare love, that comparing her to the same old images that everyone else uses actually wouldn't be good enough for her.