Because I assume that God isn't dead set on deceiving us. We have observed the bones and other fossilized remains of many more creatures that no longer exist than we have observed creatures that do currently exist. Of course, ANY idea involving an omnipotent God is not falsifiable (and hence unscientific) since God certainly could have made it look like there really were a whole lot of extinct species when there actually aren't. However, are you really denying that species go extinct?
Of course I believe species go extinct. I was just questioning how anyone knows how many have.