Are purchasing items through apps against the rules of the App Store?
Amazon and eBay are not using In-App Purchases (IAP) to purchase their products.  For instance, I have an app that allows an IAP for users to access other features of the app.  The purchases are made in the app for something that is part of the app and the users are able to pay via iTunes/AppStore payment process.

Amazon and eBay allow you to make purchases thru their apps but they're not done for things like 'no advertising' or 'add social media access'.  They're for goods and services that are not being made thru the Apple-provided buying medium, iTunes or the App Store.  So these purchases are not IAP purchases.