Sorry about this! Could you check that they're being uploaded to iCloud? You can find this out by going to Settings -> General -> Storage & iCloud Usage -> iCloud -> Manage Storage -> Show All. You should see Mini Metro in there somewhere, taking up about 8 KB.
If that is there, then at least the sync up to iCloud is working. Right now we do only check the iCloud sync when you actually start up the app, we don't when you just open it up and it's already running - we'll be fixing this in the first update. So could you try shutting Mini Metro down (double-tap on the home button, and flicking the app up) and starting it up again?
Also note that when we sync down to a device we do merge the profiles rather than overwrite the local one, so you'll keep any scores you've got on either device.