I have the same "problem". ^_~ I don't know quite how to express why it is that Dean on the bottom seems so right and natural to me, but it does, and I am the saddest ever that there isn't more bottom!Dean Wincest.

(I dunno, I'd say it's because Dean often comes off as more 'needy' of Sam than Sam is of him, or how for all his swagger he's essentially more vulnerable at times, or how Sam is far better at controlling him than he is of controlling Sam, etc, etc, but I don't necessarily see those as 'bottom' traits, so I hesitate to use them as reasons, you know? But when I think of Sam and Dean being hot for one another, it's always Sam making the first move, Sam taking control, Sam fucking Dean's brains out...)