Now even though the majority of the harem mc aren't beautiful, the reason the girls fall for them, is not appearence, but because of the personality or because the mc is someone or did something important to them. Usually harem's start with the fact that the mc is a good person, with a hearth of gold and help anyone in need, no mattering who is the person and is friendly with everyone. So he starts being friend with a bunch of girls, that lately become attract to him, because he's good for them. I would even say that in a lot of harem's, the girls matter more than the mc. The MC is more of a vehicle to give them happiness, than the opposite.
Have you seem series like Sekirei or Sora no otoshimono? I almost puked with how incredible awful they were (I think I saw one or two episodes of each), specially with otoshimono, the protagonist is the most worthless piece of shit in existence... But all the girls like him. And in others series the girls would fall for them for picking up their handkerchief or giving them directions. In other words, when it comes to harem anime, they set the bar so incredible low that is ridiculous, is a world made for them to be happy.
the protagonist of Sekirei not that bad and get better over time he's just a person with very little confidence. Who because of his repeated failures at something he should be able to easily pass doesn't seem like much at first. I don't know how the anime did him but in the manga he turns out to be a cool dude.