The movie is homophobic because they put the evil Paul in contrast to the angelic Mary (gay relationship is bad, hetero is good). When they should put Jim Hutton in Paul's place because he's listed as one of Freddie's partners alongside Mary, not Paul.
And yes the movie judges gayness and throw the gay community under the bus by swapping rockstar lifestyle label (the 70s is wild) to "gay lifestyle". While everyone in the movie who are straight are portrayed as saints mostly while they gays are bad with the exception of Jim, but he is barely in the movie at all and only had a few lines, likely just there so the movie can avoid being called homophobic. But it is homophobic.