I'm developing an App Store app which will be free to download, but there will be certain in-app purchases.
How much does Apple charge a developer for in-app purchases, if applicable?
Sadly, it depends. Did you look over the terms and conditions of tunes-connect and the marketing agreements? The fees depend on whether you are selling content through the app or the sales happen outside the app and the user signs in with an account already paid.
Take "Netflix" or "Major League Baseball season pass" for example. If you buy a subscription in the app (whether it's on iOS or Apple TV) - Apple takes their standard cut if they handle the billing and fulfillment. If a user has purchased a subscription, Apple takes no cut when the user logs in with an account and uses the app.