Suppose you and I work for the same company. I bust open Skype through decompilation, reading memory, the network, whatever trick I want. With that, I write documentation for how Skype's protocols work.
You read my documentation, and implement it in a new program. Since we haven't talked, and you've never seen a line of Skype's code, you haven't infringed on any copyrights.
It is important to note, though, that this does not necessarily protect us against a patent suit.