It means don't be hurt of offended by my comments. I am just trying to help you or make a general observation. I am not trying to hurt you with my comment.
"Don't take this personal, but that haircut you had doesn't look good".
You are trying to give advice or help to the person (their hair stylist was terrible). You are not trying to hurt the person with your comment.
Don't take this personally, but you're an idiot for doing that.
Again, you are giving advice to the person (they shouldn't have done something). You wish to be a 'little' critical of them, but you soften the attack by saying 'don't take this personally'.