The Honda Passport is only 70cc has a scooter step through design but has foot pegs. It is a semi automatic three speed with a shift pedal but no clutch. Even the chain for the drive is in a housing. With all of these scooter like qualities it is still considered a motorcycle.
Really none of it has to do with engine size because scooters certainly are common with 250cc engines. The main thing as far as I know is that scooter have no user controlled gear shifting. The second factor is styling specifically the step through design. Its not to say that there are not scooters disguised to look like motorcycles.