It appears that the Rail Business of the year is selected from one of the category winners, kind of like the winner of the UEFA Champions League comes from a field of teams that already won their regular competitions.
A close examination of the categories would show that only a few of them are explicitly related to passenger operators, with the rest being general.
What's to stop a freight operator putting in an entry for the rolling stock excellence award, perhaps apart from the fact freight operators aren't getting the money for employees to waste time on industry awards from lucrative government franchises?
Nothing like winning awards from a supposedly independant organisation which is both funded by and doing business with..... the train companies they give the awards to.
To be fair, I don't think I saw any claim of independence on the website, they are just industry awards and claim to be nothing but that.
All sorts of businesses participate in industry awards, it's not a con. In some cases (like advertising effectiveness awards) they are actually really well done, while architectural industry awards are infamous for having too much external influence. I don't know much about these awards, but the categories and criteria page looks reasonably promising as an indication that they are not incestuous back-patting exercises.