Not all extinctions were body size controlled. The meteorite impact at the K-T boundary, for example, resulted in the extinction of many taxa of all shapes and sizes. The Pleistocene extinction, however, saw the end of an astronomically huge number of large mammal species all at the same time, so body size then seems to have been a significant factor. The food chain was probably disrupted such that there was not enough food to go around. In addition, mass hunting activities by man severely affected the large mammal populations.
In summary, the large animals are successful in their own specialized realms, such as reaching the highest boughs or migrating long distances, but overall they are at an evolutionary disadvantage. They may be at the top of their food chain, but obvious ly that is not enough to help them survive as well as the microscopic bacteria have. Good things do come in small packages!