By tightly controlling the apps users are able to install on the iPhone and other iOS devices, Apple claims to offer a more secure experience. While this isn't always true (Apple's far from immune to security vulnerabilities in its software), the App Store approval process is at least intended to check apps for security holes, malicious code, and other problems.
It's hard to give a definitive answer to this question. While there have been a few instances of malicious code targeting jailbroken iPhones, but I'm not aware of there having been any well-publicized instances of apps offered through Cydia or other app stores being entirely malicious and misleading.
Additionally, despite the App Store approval process, scammers have been able to get malicious apps onto the store and users' devices.
I tend to think a process with some kind of review (even a flawed and inconsistent review) like that offered by the App Store is more likely to catch problems than a store with no review process at all.
I'd say be a bit more careful with what you install outside the App Store, but be careful with and pay attention to what's being done by any apps you install, no matter where you get them.