Hi s49,
OK, so I got my gift card, put it in my Passbook by scanning the bar code with my iPhone camera (but it also appears that it could be updated via iCloud as well), and then tried to purchase something through the Apple Store app on my iPhone. I had the same result you did - it wanted to go to my credit card.
So, I started doing some digging and you can redeem the card using the Apple Store via a computer, or via the website, but the Passbook-enabled app means only that you can purchase passbook items via the iOS Apple Store (i.e. Gift Cards that will go into the Passbook, and which can be used in an Apple Store because they have the bar code on the pass in the passbook). Here is the paragraph from the Apple site on the Passbook-enabled apps:
Passbook-enabled apps: When you buy tickets, check in for a flight, or add a card through an iOS app, the app will offer or prompt you to add a pass to Passbook. To view a list of featured Passbook-enabled apps on your device, select the Welcome pass in Passbook and tap "Apps for Passbook". You can also click or tap this link to view the list in the iTunes Store: http://itunes.com/passbookapps.
So, the app allows you to purchase a Gift Card that can then be put into your passbook. The pass itself is used in a physical store. The Gift Card balance can be used online, but the only place you can redeem the card itself online is via the website.
Hope that makes sense!
Cheers,
GB
P.S., and unlike the iTunes & App Store Gift Cards, you do not "redeem" the card and show a "balance" on your account. As you purchase items on the online site or through a physical store, if you provide the Gift Card PIN when completing the purchase, it will deduct the amount of the purchase from the card. You can check the balance by going online and typing in the PIN and it will tell you how much is left on the card. So it works a little differently than iTunes & App Store gift cards.