There is a frustration, as a user, that as the value of the iOS exploits increase, they become more and more 'underground'. The time between OS release and public jailbreak is continually growing - and it doesn't seem to only be due to the hardening of the OS. People are selling their exploits rather than releasing them publicly. And the further underground they go, the more likely they will be utilized for nefarious…
This reminds me of the PlayStation 3. It remained an un-hacked console for so long and the theory goes that the people who wanted to tinker with it could do so without being forced to fight on the same side as the bad guys, because Sony allowed 'Other OS'. When Sony closed off 'Other OS', this gave incentive for people to actually try and jailbreak the system [1].
Yet now the people that just wanted to tinker had to take the same route that people who just wanted to pirate would have to take. By locking the platform down further, Sony only succeeded in merging the two camps (benign tinkerers and pirates). I think there's a lot of validity in this theory.
It's a tough choice. As an iOS user I've long since come to the same acceptance as you - that the added security is worth the extra restrictions. Yet it doesn't have to be this way. Protecting your platform from hackers shouldn't be the same as protecting your platform from SNES emulators or games with adult themes.
[1] I believe it was this talk where this view was put forward, but I might be wrong (at work, can't really double-check): https://www.youtube.com/watch?v=PR9tFXz4Quc