When the iPhone launched, Apple had to have their own apps on there because there was nothing else. Now, the author is saying there's better alternatives to the defaults. That's true in his case. But not everyones. The App Store is full of crap. Like full of it. While Apple doesn't need to lock you into their apps, they are still selling the iOS as a great experience. They have to bundle their own apps on it to guarantee a level of quality for the user. Not all users are going to find replacements for those apps. Not all replacements are going to play ball with the Apple - iCloud - iTunes ecosystem in the way Apple wants/needs. And that last reason is perhaps why they don't let you delete.
Also, the whole Apple design ethos is that they never, never make mistakes (Of course they do, but they still act like they never do). If they allow you to delete these default apps, it's tacitly admitting that they don't belong there and/or there are better alternatives. Sacrilege!