in many ways. first of all, the exhaust which is most obvious, release lots of bad gases and hydrocarbons into the air like carbon monoxide, carbon dioxide, sulphur dioxide, methane, etc. the gases from the exhaust either cause smog, or contributes to the greenhouse effect.
another thing which isn't directly related to driving cars, but still is related to cars. sometimes people do their own oil changes. when they have their waste oil out of their car, they do the wrong thing and they dump it into the sewer or in a lake, or in the ground. this is horrible because one gallon of water can contaminate over 10's of thousands of gallons of water. water's important, EVERY living thing needs water for survival. water is the essence of life, and people are just contaminating it instead of bringing it to the store for proper disposal.
also the manufacturing of cars isn't "always" clean.