You may well be wondering how a something like an online software store can have political implications. The answer is that the infrastructure that makes it work can, at least in the ongoing war on general purpose computing. If you aren't familiar with this war, read the article.
By delivering iOS with the App Store as the only authorized means of adding software, Apple has shown that it's possible to create a popular computing platform that isn't a general-purpose computing platform. I don't believe they did this by - as Cory Doctorow claims in the above article - delivering a device with malware preinstalled. Instead, they heavily censor the software that can be installed, turning iOS devices into platforms for running a small set approved software appliances.
Implication for Apple
Computer manufacturers are normally shielded from liability for any crimes committed using their products because the computers have so many legal uses, and they can't control the software that the customer installs. Apple has lost this last claim - they exercise absolute control over the software their customers install.
At some point someone will use an iOS device and an app from the store in committing a crime. Given the deep pockets theory - which says you pay for damages depending on your ability to pay, not your responsibility - and Apples very deep pockets, some bright lawyer will decide to try and show that Apple bears some responsibility for this crime because they allowed the app to be sold in the store.
Whether Apple will lose and have to pay, or pay to make the lawsuit go away, or fight and win is yet to be seen. But the lawsuit is certainly bound to happen.
Implication for users
The unauthorized way to turn an iOS device back into a general purpose computer is to jailbreak it. That is a violation of the DMCA, but jailbreaking is currently legal because the US Copyright Office provides an exemption to the DMCA for actions required to unlock phones for use on other carriers. Since jailbreaking is required for that, it's covered.
The question at hand is - how long will that stay true once the government realizes that that exemption allows people to use iOS devices for all the illegal activities that Apple prevents? Again, the answer is unknown, but the continued existence of the exemption - which must be reviewed at regular intervals - will get less and less likely as the war goes on.
Implications for other manufacturers
Those fighting to keep the public's computers from being able to perform actions that government has been convinced are bad for the country - basically, to keep the public's computers from being general purpose computers - will love iOS and the App Store. They demonstrate that it's possible to make money building and selling computing platforms which can have arbitrary restrictions placed on what they can do.
Since Apple can do this, why can't Dell, Gateway, Microsoft, HTC, and everyone else who makes computers or operating systems? If they try and resist - which doesn't seem likely, as such stores are profit centers - I'd expect it to become a legal requirement in order to sell computers.
If you like not having the government dictate what you can and can't do with your computers, you need to support platforms that don't let anyone do that. Avoid iOS. Avoid buying software through manufacturers stores. Avoid hardware that won't let you run alternative operating systems.
In a sentence: protect your right to choose by making sure you buy and use systems that preserve it.