Friction is probably one of the primary reasons; as friction also correlates to wear. Friction is much more complicated than the equation we learned back in physics. Published friction coefficients are very much ball park figures because the friction greatly depends on the micro surface texture. This causes of friction link does a good job explaining some of the mechanics involved.
One of the main factors influencing lower friction for dislike materials is that there is a lower likeliness that there will be adhesion between them (atomically and macroscopically). A materials professor I had once lectured that if you were to polish two pure copper surfaces perfectly smooth in a vacuum and touch the surfaces together they would immediately become one piece of metal (cold welding). Similar adhesion occurs for plastic; perhaps even more so in the standard environment.
Another consideration is that plastic on plastic can not dissipate heat nearly as fast as metal on plastic, which could lead to additional adhesion wear or failure.
Sometimes the erosion of softer material is used to "dry" lubricate a surface such as oil impregnated brass bushings or graphite motor brushes.
Also, the harder material can stay smooth and true, reducing the friction and wear of the system in the long term. And like welf mentioned in the comments, the softer surface is usually a consumable (bushing, brush, etc) that is more easily replaceable.