Because different institutions have different needs. As a particular example, the Scripps Institute has an astonishingly high, >100% overhead rate, because in order to do their research, they need to be able to maintain research ships. Which are, unsurprisingly, very expensive.

Edit: Per the post below, this is incorrect - don't remember where this information lives in my head. But the general point remains the same - because different institutions will have different costs.