From the article, here's two quotes from veteran David Garrard about why smartly running the football can be so deflating for opposing defenses.
“Five or six yards is big, especially when the quarterback does it because that really drives the defenses crazy,” Garrard said. “That’s the one thing that I as well as (Antonio Cromartie) said in the game: Use your legs. You don’t understand how much the defense hates that.”It's this little wrinkle of the Jets offense that can make a big difference in a drive or a whole gameplan. If defenses are doing their best to take away all of Geno's passing options and not respecting his ability to make some yards with his feet, then the Jets can wake up a defense and make them assign a player to watch out for Geno using his feet. That, of course, leaves one less man for coverage ... it's a simple thing but it helps a fledgling NFL quarterback a chance to get the defense reacting rather than be proactive.
“As a defensive coach, you know that a mobile quarterback hurts you,” Garrard said. “It stresses your defense. You could have everybody covered — the perfect coverage — but then your quarterback takes off and gets 10 yards and you’re like, ‘Man, what else could we do?’
Asking a quarterback to run the ball can be a dangerous matter, but Geno has shown that he is decisive when he does it, has some impressive quickness, and (for the most part) does a good job of protecting himself unless he perceives no other way to get the yards he absolutely needs.