The massacre would have occurred in territories under the control of King Herod, who had been appointed "King of the Jews" by the Roman Senate. When the Wise Men refused to reveal the whereabouts of the infant Jesus, who Herod considered to be a potential rival, he ordered the massacre of all newborns figuring that this was the only way to ensure the death of Jesus of Nazareth.
I would imagine that Peter Paul Rubens would have painted a background that resembled the architecture of the buildings or temples in Jerusalem for historic accuracy. If he hadn't himself visited Jerusalem, then he may have examined the work of other painters who had and copied from them. If he didn't copy the work of other painters depicting Jerusalem, then it would be logical to assume that he relied on his own memory of Roman architecture or on the depictions of Roman architecture in the paintings available to him up to that point in his life.
I don't know enough about Rubens to help you precisely. Perhaps a good biography would narrow down the possibilities or point you in a definite direction.
