The key thing is that you can set up a separate website for payments with iOS devices, but you can't embed or link to that website within your iOS app. I've seen apps rejected because their technical support website was linked from the app and the header of that website got you to the payment website after like 10 clicks.
Of course, even if you set up your own payment infrastructure you are going to be paying somebody a cut.
Visa, MasterCard, PayPal, and Stripe et al. are going to take a cut of any transactions they process.
You have to decide if the fee they charge is worth the additional sales accepting that method of payment might bring in.