Obviously there are native app advantages to the end user beyond that, particularly given the slowness of 3G internet and the ease of making payments via the App Store. In many cases though its simply the same reason they also have Facebook fan pages and once had AOL keywords - branding.
Steve Jobs even started extolling the virtues of Apple's ability to "bring subscribers" to digitl publishers, and going by their latest announcement, Apple themselves regard their platform as being worth 30% of the value of the content, even to those who would rather process payments themselves.
It remains to be seen how far consumers and creators agree.