Margot wasn't hideous or ugly, but she didn't have that timeless beauty quality that some other Lois's have had since. She was right for the part and how it was written in my opinion. She was a feisty and headstrong Lois Lane.
As I think about it I really don't think she is ugly. It's just that smoking is one of the biggest turn offs that I know and there are a few scenes with her babbling with a cigarette hanging out of her mouth that just renders me disgusted.