It's like buying an android phone then being sour that photoshop doesn't work, I think.
As for why I'm wording it as if the AppStore will dissapear, it's because of all the reasons I laid out.
Right now it's a gate or a fence; the great filter which all must pass through; but if there exists a cheaper/easier alternative that gives the same results, why not use that? It will become incredibly normal to run the alternative app store- to the point where a lot of software will be released only to run there (which is a stated aim) and if everyone has the alternative store, why bother with Apples?
Yes, for a developer or advanced user, walled gardens look bad. But we as a community need to accept that we are a small minority of users of Apple devices. I personally recommend iPhones and iPads to entry level users in my family because I know they can't mess up the device completely without knowing ... so, to be honest, because of the walled garden and the limited choices. And I accept that if I want more freedom, I have to get something else for me.
Therefore, the question isn't why someone doesn't want to give you the choice and freedom, but why you (and sometimes I, and a lot of people in our community) want to force a change to the majority of iPhone users that are perfectly happy with the current status quo. A status quo that was in place 5 to 10 years ago and was definitely in place when they bought their devices.
But why are you wording this as if AppStore will somehow vanish? I don't think it will be going anywhere even if some apps will start working without Apple's permission. Chances are, it'll get better if it has some real competition.