For a massive majority of people, jailbreaking = install Cydia = install Installer = pirated apps.
It's a no-brainer that Apple wouldn't like that. Yes, I know Cydia has legitimate programs in it. I've used it before. But it's also perfectly reasonable for Apple to kill it all in software updates. You don't like it, don't update.
It's sort of like the R4 DS card. It has tons of legitimate, legal purposes. It's just that almost everybody that gets it uses it for illegal purposes.
That reminds me of my modified wii. I cant get the update 4.2 or it would wipe homebrew and might brick my wii