The reasoning, the article assumes, is because Opera Mini would be a direct competitor to Safari on the iPhone, and we already know that Apple has squelched other applications that competed directly with their own products. But clearly, not all browsers are built the same. People have preferences and people like to make choices about what software they use.
Could this turn into another fight between what Apple wants and what their users want? The success of the iPhone has much to do with the functionality of the phone, which has been helped dramatically by 3rd party applications. Apple might be shooting themselves in the foot with all these roadblocks in front of the App Store.