This is a great question. It is always easier to try to conserve a single species than trying to preserve the whole ecosystem. There is a simple reason for this. Ecosystems are extremely complex. There are so many variables that we cannot possible account for everything. Furthermore, there are many variables that scientists are not aware of and other external influences that might be out of control. For example, a factory or a company might be changing the ecosystem. Or it could be due to acid rain or changes in the temperature. In many cases, things are out of our control.
When it comes to single species, we vastly reduce the complexities. This is why when it comes to endangered species often times what people do is to remove that species for a time to make sure that species survives. When the species begins to thrive again, it can be released.
With this stated, I do not want to give the impression that ecosystems are not important. If possible, the best solution is to preserve the ecosystem. But in the short term, the preservation of a single species is much easier.