This apple is actually infected by two diseases. The black spots are Black Rot, another fungus and the Cedar-Apple Rust is the brownish mottling all over the fruit.
The rust has little effect on the flavor and texture of the fruit but it makes them just about impossible to sell for eating fresh.
As a point of interest, the Delicious Apple is immune to this disease and probably explains why it is so popular in produce markets in spite of it's insipid flavor.
This picture is the gall that appears on the Cedar tree in late Winter.
When this gall gets wet from Spring rains, the jelly masses emerge from the pores to ripen the spores. When the jelly dries, the spores are carried by the wind to apple trees.