This is a tough one because on the one hand, children need to learn that not everyone will like them but they still need to work with them.  On the other hand, I find this teacher to be completely unprofessional and should be called on what they said.  Maybe other parents have had similar incidents.  Talk with the teacher first and if you feel unsatified with the response, talk with the principal.

I agree.  You should talk to the teacher again and tell her how you are feeling and what your son said about her.  It's possible that there was a miscommunication.  
It is also true that your son needs to learn that not everyone (including adults) is going to like him.  It's a fact of life.
However, the teacher spoke in an unprofessional manner and should apologize for it.  She probably meant that his habits are irritating and annoying, but she should not have said that HE was annoying.
So, talk to her about how you're feeling and what you're thinking.  Only after you feel you've made a good attempt to communicate with this teacher should you talk to the principal.
It is also important that you talk to your son about his habits.  Ask him why he thinks his teacher doesn't like him.  Maybe he has habits that are inappropriate for school and either doesn't realize he's doing them or doesn't realize they are inappropriate.
Although in all reality, playing with his hair while concentrating is a very small thing and as long as he's really thinking and doing his work, it shouldn't matter that he's doing it.  If it bothers other kids, he should try to stop it, but the teacher should also tell other kids to try to ignore it if it bothers them; life itsn't always easy and sometimes you have to deal with unpleasant things.