Were you going out of your way to circumvent native functionality somehow? A calculator app probably "doesn't use much native iOS functionality", but I don't see how that would get it negative points on App Store approval.
That's your issue then. They have rules to stop the App Store being flooded with website wrappers. For it to be in the app store, there needs to be something it offers to make it worthwhile for users. If it's just a website, they can just use a web browser and pin it to the home screen if it's something they use frequently.
