The problem is that some stuff won't ever run as intended if released through the official method: Apple blocked some system calls / functions in their developer API, and the license restricts you even further on what is allowed; hence no Java (can't run bytecode), no IM (can't run in background) and no ROMs. So naturally, iPhone users will want to run the unrestricted apps, which require jailbreaking.

I wonder why Apple went down this road instead of doing something like Symbian signed, or RIM's "restricted calls" policy: some libs require the accessing module to be signed by RIM. However, Apple just states "you can't do it" flat out.