I don't think the concept of 'fairness' comes into it.
To question if it is 'fair' on Rooney, there is an implication that his being dropped is a personal decision based on a personal issue.
It is purely a professional decision based on picking the best team available, and right now Rooney does not qualify.
As a professional, he accepts this, and has said he will work to regain his place.
That puts him in the same position as every other footballer in any team from the bottom to the top.
Fairness does not come into it.