Might they want to minimise interference with the layers of dust/dirt on the ground, where possible? Probably not - maybe that's akin to explorers worrying about longboats pushing into the sand when they reached a beach...
They plan on driving a significant distance, so I don't think they're too worried about contamination of the landing site. I think the real issue is that they have many sensitive instruments and protecting against very small high velocity particles is difficult.
"These dust covers were one of the last things added to the rover. The MSL HazCams are build-to-print copies of the MER HazCams. On MER, the cameras were protected inside the lander, and in over 10 rover-years on the ground they haven't seen dust building up enough to be worrysome. The Skycrane system was supposed to reduce the plume ground pressure during landing to the point where dust wouldn't be an issue for MSL."
"But after Phoenix landed and everyone saw the pictures of pebbles ON TOP OF the pads on the bottom of the lander legs, and the legs themselves coated with a sticky looking layer of dust, some concerned folks looked at the issue more closely. It turned out there is a core flow in the Mars Lander Engines on the descent stage that stays strong all the way to the surface, even hanging at the end of the skycrane. And that can kick up a lot of dust+reaction products during the skycrane maneuver, some of which would go back towards the rover. There was a review of hardware in danger of being coated with "sticky" dust; everything was determined to be dust tolerant EXCEPT the HazCams."
I think it's mostly that they wanted to minimize any clouds from causing it to think it's closer to the ground than it is, and to keep the instruments from getting covered/clogged on landing.
