My understanding is that those passports (or other id) are used by the ship to clear immigration on arrival, so their keeping your passport does not raise issues for your New England trip. There's sometimes a port on some cruises where you need individual clearances (I remember needing it in St. Petersburg--Russia, not florida), and they return your passport to you for those. Otherwise, they're keeping it for the purpose that you usually carry one for--immigration clearance.
