I have a UIWebView that is smaller than the full screen (specifically 540×560 pixels). My issue is that my jQuery mobile content is being cut off rather than resizing as I would expect a responsive website to do. I’ve uploaded a sample project with the issue here. Any ideas how to fix this?

Set the width and height of the viewport to whatever the height of your UIWebView. This will register the “bottom” of the browser window and should prevent your content from being cut off if it is the appropriate height.
See here: http://developer.apple.com/library/ios/ipad/#DOCUMENTATION/AppleApplications/Reference/SafariWebContent/UsingtheViewport/UsingtheViewport.html