Even though Apple has claimed they are working to improve their App Store submission process, developers are still finding themselves blocked for seemingly arbitrary reasons. Recently, one developer found himself at the receiving end of rejection letter from Apple due to his app being related to torrents. Though any tech worth their salt knows that torrents have come a long way from nothing but pirated content, Apple seems to believe otherwise. As a result, they rejected the "Drivetrain" application on the grounds that it may be used to infringe third-party rights.
The information from iLounge is still somewhat limited, and more specific details about the situation aren't yet available. At the surface, though, it seems that Drivetrain, which is merely a remote control for the Transmission torrent client on Macs, is currently on Apple's blacklist. If Apple wants to go that far, they might as well restrict torrent apps on the desktop or say that VNC clients aren't allowed, since they could be used to remote control pirating machines.
Ultimately this is all coming back to the same point: Apple wishes to retain total control over the iPhone, which they see as their phone - not the user's phone. It is a pity, as they have crafted one of the most unique and important modern computing devices. Why impose artificial restrictions on yourself or your users?