The Average Rating measures the overal quality of a product based on an average of individual critic scores. The Tomatometer simply measures the percentage of critics who recommend a certain product.
For example, while Men in Black scored 91% on the Tomatometer, the average rating is only 7.5/10. That means that while you're likely to enjoy MIB, it wasn't a contender for Best Picture at the Oscars. In contrast, Toy Story received a perfect 100% on the Tomatometer with an average rating of 9/10. That means that you are not only certain to enjoy it, you'll also be impressed with the direction, story, cinematography, and all the other things that make truly great films great.