She is not hideous by any means, but she was terribly miscast, in my opinion.
Supergirl, like it or not, has expectations and how she should look, and those are very high. She has consistently been played by very beautiful women. Or drawn as one, if you count comics and cartoons.
I think most people calling her ugly is due to people getting a whiplash for her failing to live to those expectations. Even average is not enough to meet them. So I think it's less her being a hideous monster and more like she is not pretty enough to be Supergirl, which I do think it's the case.
When she is compared to the other live action Supergirls she easily stands out as the least attractive. Even compared to the one that showed up in the Flash movie.
Milly would had been better suited for another role.