I think you're mixing up ships. There's very few fans who actually think that the actors who play Dean and Castiel are really sleeping together. Those are two very different sections of a very polarized fandom. In fact, most of the Dean/Castiel shippers hate the Jared/Jensen tinhatters, and most of the Jared/Jensen tinhatters hate the Dean/Castiel shippers as well as Misha Collins and the character of Castiel.

Misha and his wife are openly poly and on that basis I have run into a couple of people who say that it's possible that Misha and Jensen were together. The assumption is that their significant others would have okayed it. So there's a very different vibe to it.