Your passport is the most important travel document, so it's probably best you don't just shove it into some random compartment in your bag. A good passport case might be the ticket, or you could keep it nice and safe inside Best Made's new Bonded Canvas Passport Case.
The case is made from a 10 oz, water-resistant duck canvas with a 7oz bonded flat twill interior with taped interior seams. It's got room for pens, small items, and of course, a discrete document pocket for your passport. A substantial brass zipper keeps it all locked down and secure and when we're talking passports, you shouldn't have it any other way.
$54, available at bestmadeco.com.