I have the same .... I am able to get the dirt/rust? off . I don't feel it is rust ..because surface rust doesn't usually form like this.
It appears to be more like mold/mildew. or road grime? In any event I used a
prep solvent followed up by a liberal coat of cleaner wax. let dry very hard.... then polish off. An old tooth brush helped me out too.
It appeared like rust to me originally. I don't believ it is. My 06 HL gets waxed 3 times per year with spray waxing between .. after every wash(usually once per month). I can't see how it is rust. At least on my HL.
The thick 3M clear chip guard that yu have allows dirt to collect at the edge. I would not remove it unless yu replace it. And Toyota gets stupid money for this part.
I have the OE
running boards so this clear protector doesn't really do anything. The boards keep the road chipping at bay. If yu don't have the R' boards I would keep the protector there.
Just my thoughts.
LT