It's fair precisely because they don't run. That's like saying "how fair is it to include YPA and Touchdowns to the other 20 QBs who don't throw deep like McNabb?". Look it's not McNabbs fault Brad Johnson has a weak arm and it's not Mike Vicks fault Drew Bledsoe can't run around.
QB Rating is designed to measure QB contribution. Vick running is a contribution. Drew Bledsoe getting sacked is a contribution (negative). Gradkowski fumbling is a contribution (negative). Those things should count.