Because your making money of someone's else portal that they created. Sort of like when sales person works with a customer for awhile and then another sales person comes in an snakes the deal away.
I think this is where most people get mixed up, confusing the platform for the app store. The iPad is no different from a Windows machine or a Mac. When you're running Kindle on OSX, Amazon isn't sneaking into Apple's store and stealing their customers. They're offering up another storefront for certain goods and services on Apple's platform. Like I've been saying previously, Apple doesn't owe MS anything because they're offering people iTunes on Windows, so why should Amazon, Netflix, MS, and the rest owe Apple for doing the same thing?
Keep in mind that 3rd party services make the platform more appealing to customers. There are some people out there who bought an iPad to read their Kindle books on. If they didn't have that option, they might've gone with an Android tablet. There are probably even more people who like watching Netflix on the iPad. If Netflix wasn't on the iPad, then...well...they'd probably go with Android.
Third party services aren't leeches greedily sucking the lifeblood from Apple's customer base. It's very much a mutually beneficial affair. Apple provides a popular platform for 3rd parties to make money off of, and 3rd parties make the platform more appealing by offering more options.
Now I agree that Apple deserves a cut for any service they provide. Hosting on the app store? They should get their 30% cut. Same with any hosting or payment processing fees. But when it comes to the service itself, Netflix's subscription fees, Kindle's books sold off their own servers using their own bandwidth, things Apple has no part of, they don't deserve a dime. Like if Zynga uses the app store servers and payment setup for their IAPs, then Apple gets their 30%. For something like Netflix, not so much.