Apps just aren't very well integrated into the paradigm yet
The gift card thing is just part of a more general issue, which is that Apple hasn't really integrated apps delivery very well yet with the iTunes concept. No doubt they'll refine it in time so let's have patience with them. It's very smart of them to use the iTunes transaction mechanism to sell materials other than music but for the uninitiated it's rather confusing, starting with the name - I mean, you'd expect something called iTunes to be selling, well, just tunes, wouldn't you?!
There are several oddities with apps - for example, if you try to buy an app in the iTunes App Store by just clicking "buy" it gives an error message "Applications cannot be purchased with the Shopping Basket - select "Buy" if you would like to purchase by one-click". This is complete gobbledegook for a new user who just ambled in for the first time to buy an app for his new iPhone and never had anything to do with iTunes before.
Another oddity is that if you're in the iTunes App Store and you do a search, you get a list not just of apps but also of music tracks and movies and things. The app entries quote parameters like "artist" and "album" which is just the wrong terminology for an app and is, again, confusing for the average user. Poor user interface design.
Geeks may think such user-interface niceties are trivial non-issues but that's just because they're, well, geeks