Apple's made a very opinionated choice in choosing what software to allow on the AppStore. On the Mac this isn't a fatal problem for developers due to the ability to side load applications. It’s the fact that apps can't be side loaded on iOS that causes the real damage (imo). But I also think Apple should be able to run their app store as they see fit.
Apple seems to be trying to figure out a way to have it all. They want a vibrant developer community without the all of the hairy cruft that comes with true choice, like viruses and malware. Again, imo, they lose something by forcing this choice down everyone's throat. They create too much friction for developers. There is that bottom-line terror every time a dev thinks about writing an app for iOS: will Apple allow this app to exist? To me, this is a horrible and limiting thing to have to even consider and the reason that in the long run Apple will have to give this idea up or see their platform slowly fade over time.
I'm torn, because I am glad that my Mom can be relatively safe when running her iPad with its limited selection of apps. But the idea that I have to think about whether or not an arbitrary person working at a huge multi-national can terminate my idea for an application is just too much freedom to give up.
Not sure what the answer is, but official app side loading would go a LONG way (for me) towards reducing that friction.