There are multiple ways to monetize your applications, and they are all described in Apple’s website. Most business models are using Apple In-App Purchases because it is easier for the user to buy something after having tried an application. In addition, In-App Purchases is the only way to support Subscriptions in your application. To monetize your application, you will need to either release it as a Paid application or support Apple In-App Purchases. There are also hybrid business models which are presented in Apple’s website.
Apple will not allow the use of different payment methods like a credit card, PayPal, Stripe, etc. in your application, except if the payment is defined in section 3.1.3 Other Purchase Methods of App Store Review Guidelines