Complexity begets attacks. Apple's policy is "no rootkits". Allowing the user to modify the system software is basically a backdoor, and backdoors have an undeniable history of being abused by people other than their intended users.

Apple sees the iPhone as a hardware security device. Apple wants users to be confident enough in its security that they can use their phones to authenticate financial transactions.

It's great that some phones are modifyable by their users, but I would never ever link my Android phone with my bank account.