Apple does not agree to abide by your terms. Instead, by clicking "I Agree" when you submit a new app, you (app submitter) is agreeing to abide by Apple's terms. That's an important distinction in this case. It's irrelevant if you'd like Apple to change their polices. (Though they may some day - they've changed and relaxed many things over the years.) The point is that someone told Apple they had all legal permissions required to allow Apple to distribute it the way they do, and since there was an actual legal contract involved, Apple trusted that person. That person was apparently mistaken. It is that person whom the FSF and/or the VLC dev should be angry about - not Apple. (At least in this case.)
Yes, Apple's policies are calculated. That doesn't make them evil nor does it make them necessarily wrong. It sounds to me like you want your (GPL, etc) rules to trump Apple's rules. What gives you that right? The App Store is huge, popular, and everyone wants a piece of it. Apple created that success for themselves. You (or anyone else) has no basis to rush in and claim they deserve their own little slice of it just because. You play by Apple's rules until Apple changes their rules or don't play at all. Don't like it? Go somewhere else - that's your right which is given in exchange for Apple having the right to make their own rules.
No, it is Apple you should be upset at. They're the ones who set up the store which requires everything to be distributed under their EULA, and they're the ones who don't allow you to install any software in any other way.
If you take away one of those restrictions, great! If the App Store isn't the only way of getting software onto my own hardware, then they can have whatever policies they want; I can just get the software from elsewhere (see, for instance, Android). Or, if they actually abided by the terms of any free software licenses for software they distributed, well, less fine (I still would like to be able to get my software from elsewhere), but they're at least complying with the terms of those licenses.
So yes, it's disappointing that someone clicked "agree" to something they couldn't legally agree to, because it violated the terms under which they were distributing free software. But Apple is the one here who is significantly restricting end-user freedom; and the point of this sort of enforcement of the GPL is to get the point across that free software developer will not let Apple benefit from being able to distribute said free software without complying with the terms of the license.
Apple benefits from having a better selection of software in the App Store; if I can play my videos on an Android phone, but not an iPhone, that might help me decide in favor of Android. They shouldn't be able to benefit from this without complying with the terms of the license. There are several free software packages (like VLC, GNU Go, and more) that they could benefit from, but should not be able to until they stop restricting end user freedom.
I am not trying to get "my" rules to trump Apples. I am trying to say that if Apple wants to benefit from my work, then they must play by my rules. I don't use or develop for iPhone for just this reason; because Apple isn't willing to play by a set of rules that I agree with. I have an Android phone; while it isn't perfect in respecting end-user freedom (it doesn't come with root, and rooting it voids your warranty), it is a heck of a lot better (I also use a Mac, for instance, which while much of the software is not free, Apple does not restrict what software I can an cannot run on my own machine, which I consider an acceptable compromise).
Yes, Apple's policies are calculated. That doesn't make them evil nor does it make them necessarily wrong. It sounds to me like you want your (GPL, etc) rules to trump Apple's rules. What gives you that right? The App Store is huge, popular, and everyone wants a piece of it. Apple created that success for themselves. You (or anyone else) has no basis to rush in and claim they deserve their own little slice of it just because. You play by Apple's rules until Apple changes their rules or don't play at all. Don't like it? Go somewhere else - that's your right which is given in exchange for Apple having the right to make their own rules.