Of everything that irks me about the app store (and I say this as someone who uses almost exclusively Apple computers / mobile devices), this is pretty high up there. It makes it damn near impossible to run a successful marketplace businesses on iOS: if your business is based on skimming a percentage fee off the top of your user's transactions, Apple taking 30% is more often than not a dealbreaker.
That being said, that's not an issue of native apps vs. web apps. If you want your application distributed through the app store, anything payment-related (or even potentially payment-related) needs to go through Apple's payment services. Period. Apple would complain just as much if you had a native app that had your own payment form, and they'd be 100% fine if you built a pure webapp (i.e. not on the app store) that accepted non-Apple payment.
That being said, that's not an issue of native apps vs. web apps. If you want your application distributed through the app store, anything payment-related (or even potentially payment-related) needs to go through Apple's payment services. Period. Apple would complain just as much if you had a native app that had your own payment form, and they'd be 100% fine if you built a pure webapp (i.e. not on the app store) that accepted non-Apple payment.