I think I understand what you are saying..
For example: Muslims believe torture is Ok for non-believers, even death. They have less feellings for human rights than an atheist probably would.
In the past Christian religions have been the same.. Burning non believers alive, or beheading..
AS more non-religion affiliated human rights groups were getting involved in the modern age, we have become more humane in our treatment of each other. The Pope wasn't present at the Geneva and Hague conventions.. the Red Cross/ Crescent, though many members and volunteers are religious, it is not a religious entity and has more to do with guaranteeing humane treatment of others than any church has ever done.
Take religion out of the picture, and it seems we treat each other more humanely. Take the way the US (the country as a whole) treats prisoners and POW's, and how the people expect their country to take care of the same, compared to how the Muslims, Iran, Iraq, Al Quead, and even Saudi Arabia (led through religion and the Koran) treat their prisoners.