I'm not sure that I agree that the majority of the characters don't make that association.
In 109, Emmett's whole storyline is about how he's pretending to be a "beefy, brutal top" online when he's really a "big, nelly bottom" in real life.
In season 5, I'm pretty sure that Ted makes a fairly big deal of the fact that he's the "top" in his affair with Troy when he was the "bottom" during the pity fuck in pride 2002.
Drew would likely associate being a "bottom" with being a "fag." Maybe that changes once he comes out.
Brian clearly associates being a "top" with issues of dominance and control.
So half the characters right there associate their sense of self and identity with being either a "top" or a "bottom."
Justin is the only character besides Ted that we ever see in both positions (other than that one time with Brian).
While I agree that it shouldn't make any difference whether you like to penetrate or be penetrated, I think that the writers of the show do make that distinction in how they depict their characters.