Did religion cause conflict in the classical era?

Because the Greeks and Romans were polytheistic, they tended to be a bit more easygoing about religious disagreements; after all, there's room for more gods! Of course, they also didn't need much of an excuse to wage war, and had far fewer of the moral qualms about killing people which the concept of 'holy war' was developed to overcome.

A notable exception to this was the treatment of Christianity by the Romans; because Christians were so vocal in their monotheism, and in condemning the idea of multiple gods, they were seen as a threat to Roman religion (such as it was, by that point) and were duly persecuted. Most other cases of 'religious' conflict, such as the Greek conquest of Judea (Palestine after 71 CE), were driven more by pragmatic fears of the religion serving as a rallying point for rebellion than any religious sentiment on the part of the conquerors - justified fears, as it turned out.