Interesting thread.
I was a very shy child, and moved on to being an unconfident teenager who was horribly bullied at school. I used to describe myself as an ugly duckling, as I genuinely believed that until I was in my early 20s I was actually unattractive. By the time I left school, I honestly did not have one school friend. However, looking back on old photos I can now see I was actually pretty good looking.
In my 20s, I gradually became aware that I have actually been very lucky in the way that mother nature has put me together.
I also learnt how to get on with people and to make friends. I am still by nature quite shy, but have learnt to act as if I am not. I now am actually quite good at achieving a casual friendship with work colleagues etc, and being a core part of a social group (which still surprises me from time to time).
I still find it difficult to move on from casual friendship to a true close friendship, although I do now have a small number of really close and genuine friends, which makes me very happy.
However, I have had three experiences of the sort the OP describes. One from someone who is now a good friend, who admitted that his opinion of me really changed from his first impression. He said that he assumed that I was quite arrogant and wouldn't want to be my friend, until he realised I was making a real effort to be friendly to him. We are now good friends.
The two others were both female work colleagues, from whom I got really negative vibes from the outset. Despite my best effort to be friendly, we never became friends. Both of them, at their respective leaving dos made really personal and judgmental comments about my appearance. I have also had a male friend of a friend quiz me about whether I have difficulty with men being intimidated by me, to which I honestly replied that I had not noticed. My closest female friend also once said to me that one of the good things about me is that I didn't act like a good looking person.
To the OP, I would say that there will be people who will form a judgment about you because of your looks, but you can guarantee that they will be judgmental in a superficial way about other people too. It is not realistic to expect to be friends with everyone, sometimes because they are not nice people anyway, and sometimes because they are just not obliged to like you. The only thing you can do is to be as friendly as you can I people and try to conquer your own shyness so it is easy for people to be friendly to you. Don't use your looks as an excuse not to work hard at being friendly. If you keep this in mind, you will make genuine friends, and this is far more important than being the most popular person at the school gates.