With Scott taking a beating, Rodriguez has been forced to find a balance between keeping him healthy and running a read-option offense predicated on the quarterback's ability to keep the ball and run it himself.
One of the nation's top rushing quarterbacks the first three games of the season, Scott has 38 yards on 10 carries the past two.
"I think Matt understands that we're trying to protect him," Rodriguez said, "But at the same time, we're trying to run our system."
It doesn't get any easier for Arizona this week.
Up next is a road game against No. 18 Stanford, one of the biggest and most physical teams in the country.
So far this season, the Wildcats have played teams that rely mostly on speed and spreading things out. The Cardinal play more like a steamroller, running right over teams with their huge offensive line or throwing to their oak-sized tight ends.
For a team that's a little worn down, this will be a huge test.
"They're definitely a larger team," Arizona defensive lineman Tevin Hood said. "The offensive front isn't sloppy big; they're just big, confident guys. We just have to play low, maintain a low center of gravity and hit them in the mouth."
The good news for the Wildcats is that they'll get a break after Stanford.
Of course, after that it starts all over again, the remaining schedule including games against No. 23 Washington, No. 13 Southern California, No. 25 UCLA and rival Arizona State.