Well, then Queen doesn't have the rights to make anything on it, do they?
That doesn't have anything to do with the movie production. Presumably they receive royalties from Sony, who purchased EMIs catalog in recent years. They have certain rights when it comes to the songs/albums. But I don't think they were prepared for the movie industry's notorious 'creative accounting'. This is why movies like Forrest Gump become legendary for *never making a profit*, and why star power is determined by one's ability to negotiate huge up-front salaries and *gross* profits, never *net* profits. Because somehow, magically, hit movies have a hard time showing they made any money.
Director Bryan Singer gets away with it because he's been making hits for a long time and knows the right people. He gets paid seven figures even if he abandons the set mysteriously for weeks without warning (which he did during Rhapsody AND X-MEN), gets replaced by another director, and despite being known for liking young... toys. That's the movie business for ya.