I know that the linux exploit is again, not ideal for the masses, but it gives us far better access to the Wii U hardware then the Webkit Exploit does in its current state. It bypasses the Wii U's operating system altogether (including the IOS Kernel, which is a big part of what is keeping us from getting anywhere with the Webkit exploit at this point). This gives us quite a bit more freedom when it comes to running custom code (designed to run natively in linux of course).
It does bypass the Wii U's operating system, but this is because it runs in vWii mode. The security system won't be there to stop us, but we don't get access to any of the the extra hardware, which is the entire point of running in Wii U mode.