I have to disagree. I took several mileage runs last Fall in anticipation of taking the family on a holiday this summer. On all of the flights I took, there were plenty of empty seats. My "cheap" ticket was not preventing a higher paying passengers from flying. The true cost of transporting me was a tiny fraction of what they earned from my ticket. If I had not gone on those mileage runs, the airline would have lost even more money!
Several things to also note: My frequent flyer miles that I got from those flights were used for free tickets but these seats were capacity controlled. Just becuase flights look full does not mean every passenger is a revenue passenger.
I have always heard that the full fare passengers that account for 10 to 15 percent of the passenger load account for no more than 35% of the total revenue. I realize that is still a large chunk but to say mileage runners do not help the bottom line is absurd.