As a woman, I prefer attractive male main characters... or female, for that matter. It might be shallow, but I can appreciate "ugly" characters as well... Michael Wincott was my first ever actor crush when I was 15. Even my mom asked me "... why??". Heh!
For some reason, John Marston is called ugly by many characters in RDR and I'm perplexed... he be fine looking! His son did NOT inherit his father's good looks though.
It isn't wrong other than in the minds of people MAKING it a problem... It's been true for entertainment for a loooooong time, good-looking characters are welcome.
It is equally not wrong if a character is designed ugly, the story is what makes or breaks a character and pretty doesn't equal good character development *cough* Michael Bay movie female characters *cough*...