He feels love for her, however, he still feels like she's just as rare as any other woman described by such an exaggerated term such as 'Goddess,' which is more than likely never true. From his description of her eyes being unlike the sun and her lips nowhere close to being as red as coral; her hair is like black wire, and her cheeks are not a rosy red/pink, he's stating that she's not the prettiest of women.
Nonetheless, as I have stated, he loves her for who she is, despite his charming but awfully blunt sincerity towards her appearance. You can deduct this from the very words he had written in lines such as these:
"I love to hear her speak, yet well I know / That music hath a far more pleasing sound."
"And yet, by heaven, I think my love as rare / As any she belied with false compare."
So, a simplified version of the answer; He is very honest with her but he feels a strong love for her. You can tell this from the terms of endearment he uses towards her, such as "My mistress" and "My love."