Gross isn't everything if your budget is a lot higher than those other films. Star Trek and Into Darkness have the highest-budgets of all the films even with inflation save maybe The Motion Picture.
The studio is comparing these films to other modern blockbusters and not to older Trek films. Paramount wants to hit that Avengers/Star Wars/F&F level of $1 billion. Pegg said in an interview that that's what they're trying to do with Beyond.
In this day and age, if your big-budget blockbusters aren't making at least $1 billion, there's always room for improvement, at least that's what studio heads would think. They want to turn Star Trek into one of those franchises.
Honestly, if that were the case; they would have stopped after STID. The fact is the recent films are doing VERY well for the studio.