I doubt it's leather unless they changed it for 08. My MY04 is textured black plastic.

 

To the OP, that piece is NOT leather. Even the portion that has the "dimples" is still plastic. If you look in the driver's and passenger's footwell, right where the knee would hit, is also "dimpled" plastic that LOOKS like leather, but is not.

Anyway, I also have some scratches on that area, and I simply try my best to avoid it. Maybe some sort of clear adhesive? Something similar to the clear bra you'd put on the front of a car?

I don't know. In any case, the piece is rather cheap, so if it got really bad, you could simply replace it.