The basic problem with the ESA is that it doesn't consider relative costs and benefits of species protection.
People tend to anthropomorphize mammals and birds particularly.
Demand for protection of most other species is low. There are 30-100 million species on Earth, of which only about 1.5 million have even been named, and we have no accurate measure of how many are going extinct each year. Extinctions are integral to natural evolutionary processes, but there is little doubt that human impacts on the environment have greatly accelerated rates of extinction. Each species embodies huge amounts of genetic information, some of which could have enormous value to humans in the future. Most Americans implicitly subscribe to this ethic, but limited funding for the ESA simply won't let us save everything.