Willie, yea, your missing something. I'm using passbook for Starbucks (as of yesterday), fandango, target & sephora. They all show up in passbook although I haven't deleted the apps, I probably could because I probably won't use them now. Well, yea, I need the starbucks one to reload again.
So, for 'certain' apps, you can probably just use passbook. But for the ones that you use that has a balance, that might still require using another app to reload it, hopefully in the future passbook will do more, I don't see why they wouldn't build on this.