Most Helpful Girl
It means they're hot but they don't act like the "typical" hot person. Hot people are stereotyped as being narcissistic and conceited (which isn't true), but when someone meets a goodlooking person with a good personality they say they're hot but don't know it.
Personally, I think it's a stupid thing to say. I know plenty of people who are hot and aware of that fact, yet they're not a**holes in the least.