Just using the wrapper won't let Prototype use the $ function. It's only important in pages that use more than one library, or that need to use the $ for some other purpose than jQuery for some reason.
As I said, plugin authors use the wrapper because they have no idea which pages their script will be used upon. So it's a safe way to make sure that no one steps on the $.
I personally prefer using jQuery over the $. I had to use conflict mode since a homegrown library uses it, even though we are phasing out the home grown library, I do not think I will switch back. I think it is easier to read and understand.