I am not surprised it only got two nominations. After doing some research via IMDB, I've collected that whenever they nominate serious Oscar contenders like this movie, they usually only give it one or two nods (i.e., Boys Don't Cry, Million Dollar Baby, Monster). Granted, they gave Titanic and Pulp Fiction awards for Best Movie but those films were very different from my examples above (and Brokeback).
I voted for it a few times just to support the movie but that site is so slow. And the Mtv awards really aren't imporant anyways; they're just light entertainment... I still think Brokeback is above every award there but that's just me.