I've noticed a lot of the newer cars are coming with a black plastic lower half on the rear bumper near the exhaust ports.

Lexus did it with the is250/350. Porsche Cayman has it to name just 2 off the top of my head.

I think it messes up the lines of the car and especially if the car is painted non-black. Is there some special reason 'm not aware of?

 

The reason is likely visual. If they paint the lower part of the bumper black, it can give the impression of a smaller (less tall) rear bumper, especially from a distance, making the car seem sleeker. It allows the manufacturer to lower the rear bumper (lower rear skirt), making the car more aerodynamic but without seeming to give the car a larger, fatter rear bumper.

A black lower bumper may also hide damage better than a body-coloured bumper cover. As the bottom of the bumper cover is lowered to create a lower rear skirt, it is more likely to be damaged by road spray and hitting kerbs; but if it is black that damage may be less visible.

 

It gives a better visual termination line, as well as offering a smaller, easier to swap piece for different trim levels. Manufacturers who offer engines with 1 exhaust or dual can simply change the rear valence. Sportier trim levels can add mesh in the valence.

 

I agree with Sulu. Often it is done to prevent or hide paint damage.