The amazons were made from the reincarnated souls of dead women, remember. They weren't created from whole cloth by the Patrons - they were drawn from the Well of Souls and given new bodies. So as they exist now, they have no fathers, nor mothers either, really; they sprang from the water fully-formed at the behest of the five Patrons. But as they existed pre-reincarnation, they were as human as anybody else, with two genetic parents each in the normal fashion.
Byrne, at the end of his run, introduced the bit of canon that Hippolyta's father, back before her reincarnation when she still had one, was Ares. This was yet another of his lame, ill-fitting pre-Crisis callbacks (which pre-Crisis idea itself was a lame, ill-fitting graft of greek mythology), but it has been referenced more than once since, if only in passing.