I think for the most part fandom has come to respect the fact that she's Jensen's wife, but there are still some die hard haters out there.
I mean sure I ship J2, do I think they are a real couple, no. Do I think there will ever be a chance they will become a real couple, no. But I mean look at them, how do you not ship that?
I respect both of their marriages (and I do fangirl over some J/D pics), but my shippy heart will want who it wants.
Like you said, if they are happy, I'm happy.
Did Shawn and Belle ever get back together after Shawn/Mimi?