Their physiology may seem very different from the outside but the genetic and molecular mechanisms are remarkably similar between zebrafish a humans. It's important to note that the vast majority of medical research is not "physiology" in the sense of studying whole organs or systems but rather molecular. So most research focuses on the genes and proteins involved in causing diseases and these are very similar between humans and zebrafish (about 70% shared genes). For example a gene that when mutated in humans causes heart defects may also cause similar defects in zebrafish (even though they have two chambered hearts while we have 4 chabered). If we mutate or remove that gene from the fish and indeed find that it causes heart defects we can use the fish to try to figure out how it causes those defects and potentially treat it.