FOUND! Link in comments.

I believe the story starts out with Sam and Dean in a bar, but they leave and some guys from the bar follow them.  I think the Impala breaks down or for some other reason Sam and Dean stop on the side of the road and the guys from the bar catch up to them.  They force Sam and Dean to have sex...I think it was Dean forced to rape Sam and he gave in because it was either him or the other men and Sam asked/begged for Dean to do it.

Afterward, once they've gotten away and are in a motel room Dean makes sure Sam is okay then he calls John and tells him that he raped Sam, not mentioning the reason he did it or that Sam was...sorta?...willing.  John goes to the motel ready to defend Sam from Dean only to learn the actual story.  He later goes to the same bar his sons had been at and overhears the men bragging.  Somehow he gets them alone, lets them know he's their victims' father, and gets revenge on them...I'd like to say he kills some, if not all, of them but I'm not sure.

It may have led into a continued relationship or have simply included implied prior non-brotherly feelings between Sam and Dean or possibly it had neither.  And I think it had at least two chapters but could also have been a oneshot.
I thought it was on fanfiction.net, Sinful Desire, or Sam/Dean Slash Archive but have been unable to find it...unless I'm just missing it.

Thanks in advance if anyone knows it and where to find it.