The passport decides which region you go to first. So if you start in Kanto, you get the Kanto passport. The passport has no further use. Once you collected all 8 badges in Kanto, you will be able to go to Jotho and beat the gym leaders there as well.
You won't get a Jotho Passport item, but it is only there for the game to decide to which region to spawn you when you choose your starter Pokemon. So doN't worry, you will have access to Jotho as well