Sounds like the saddle is at a good height - you won't be able to put your feet on the ground while sitting on the saddle, maybe pointed toes.

While it's true that a properly set up bike shouldn't hurt, your body has to get used to cycling and that process does hurt so in the early days, it can be hard to tell if something is hurting because of poor setup, poor components or poor fitness, sometimes a combination, sometimes all three. Best tip is to make friends with your lbs and ask them because bike fitting can only be effectively done in person.