I had the same problem when I made some snack bags and sandwich wraps for my daughters to use for school. I opted for rip-stop nylon as the interior fabric and a cotton on the outside. I haven't heard anything negative about the use of nylon (yet) so all is well. The nylon is water-resistant, not water-proof, so we have stuck with mostly dry items. They wash and line dry very well!
I love the idea of zippers. I used velcro and the crumbs in the loops drive me nuts!!!!!!!