The Rio Grande normally painted their freight stock, including cabooses, one color, top and bottom. Trucks and underframe were the same red as the rest of the car.
Modelers seem to instinctively paint the underframe and trucks black. There is no prototype for this. It does add a "shadow" effect which somehow looks good in the artificial light we generally use. For a contest model go with red - unless you're doing a stock car, of course!
Railroads did not paint wheels and axles. They were left to rust naturally. A rusty wheel looks a lot like a red painted wheel so modelers sometimes paint the wheels either red or black. Should be done with red oxide to simulate rust. Couplers the same. No paint.
Hope this helps.