The use of Romanus Pontifex to justify slavery is a good example of people using religion to justify their acts. If you read this essay by Fr. Joel S. Panzer, The Popes and Slavery: Setting the Record Straight
, you find that even before the said decree slavery has been condemned, just as not long after the colonisation of America, in 1537 Pope Paul III issued an encyclical against the injustice done to the natives in America. It should also be noted that the United States has never been under the rule of the Pope.
Seeing others as non/sub-humans is not a specifically religious but a general human attitude. In fact it is a basic Christian idea that all humans are capable of being saved, thus it was naturally the position of the Roman Catholic Church that the people of foreign lands are humans and can be converted. Nevertheless, this is not even the case of a religion causing war.
From a Buddhist perspective, violence is from greed, hatred and ignorance. Greed for others' possessions, hatred against those we don't know and ignorance about the law of karma. Christianity, as a religion, teaches contentment, love and divine punishment. Same can be said about Islam. So to me it seems to be a more complex issue here than just saying religion causes war.