Some people have a rule in their house that people may keep their shoes on downstairs, but not upstairs. In a similar manner some people require only overnight guests to remove their shoes.
I understand that the upstairs is a more intimate part of the house and the place where sleeping is done (so a natural place to keep allergy-free). However, I really do not see the need to only go half-way on the shoes-off policy. Who wants a clean carpet upstairs and a dirty one downstairs? Besides most peoples' children will be playing as often on the floors downstairs as the floors upstairs.
It seems much more simpler and straightforward to have the whole house shoe-free.