Sorry, this is gonna be long:
Of course it can be a negative. I wrote something about this recently. The fact is that when you fall on either side of the spectrum, where you're considered "ugly" or "beautiful" you will never quite be treated as a human being by the majority of people.
It all deals with shallowness. In all honesty, there is nothing wrong with appreciating and being sensitive to beauty, but most people simply cross that line into shallowness and that's when it becomes a problem.
I used to be horribly overweight most of my life so I know what it's like to be on the end of the spectrum where people consider you "ugly." I have also been in the other side of that spectrum where I've been labeled as "good looking" (and really, it's just a label some people have put on me, not the way I see myself). And the treatment is basically the same: no one takes the time to get know what is behind that image.
The only difference is that when you're considered "ugly" (and I put the word in quotations because it's not really a word I think has a true definition) people treat you with rejection. When you're considered "good looking" people just want you for a single night. Of course that doesn't apply to every person you run into. There are those with enough strength of character to search into someone else's personality, ideals, etc.
It's a bit depressing because the fact of the matter is that while looks are important on some level, it's even more crucial to be open to what is behind it. The person beneath the outer image is the most important part of it all. Shallowness is a curse upon the world that keeps us as human beings from ever exploring anything too deeply or experiencing things on a more fulfilling level.
I know people that don't understand how or why my friendship circle is so wide and includes so many different people from so many different walks of life. All I hear from these negative people is something along the lines: "why are you friends with such-and-such? He's so ugly" or "yeah, he's hot! Totally worth keeping in touch with." And I sort of just tell them: "He's a good PERSON; you'd know that if YOU weren't so focused on what they looked like and made an effort to get to know them. Your'e missing out on a great friendship and great lessons they can teach you."
I learned to see value in every human being. Sure, you can't fall in love with everyone and sure there are some that never stop pushing your buttons, but every has something to teach us and when we let the focus fall purely on looks (whether the person is "hot" or not), we miss out on that.
I say, there are disadvantages to being considered "beautiful" as much as there are to being considered "ugly." So be whatever you want to be, because at the end of the day the people that really matter will love you regardless. That's real and genuine.