To some extent, there are privacy and trust issues in both places. But I have a bit more confidence in Apple's ability to police their store, and more importantly, official apps are sandboxed and can't touch the filesystem or OS directly.

But honestly, I'm more concerned with quality than trust. I think that malicious apps are probably very rare on Cydia; I'm more concerned with background processes that eat battery life, changes to the underlying OS which make the phone unreliable, buggy code with unintended side effects, etc. I don't think this is the norm, but I have very little information with which to separate the gems from the junk.

On a computer, installing apps with no restrictions is the norm, and so there are countless forms of social proof to discover which apps are safe and reliable. I'm looking for something equivalent for Cydia packages, as well as detailed manifests of what is installed and running with each install. (Perhaps I should just stick to paid packages, where the author has higher incentive to maintain quality.)

Disallowing access to private APIs does at least offer some amount of protection against flagrant theft of personal data.