Imagine a bajoran vedek having the chaplain job on a ship, could someone from earth relate to him? After all his "gods" are real, you can literally visit them, there's no doubt that they exist, even if you consider them to be just wormhole aliens, you know they are real. .
Even with this in mind I still believe that there would some atheists on Bajor. There were a lot of doubters up until Emissary. Some people never had a vision when they visited the orb. To my knowledge you never heard Ro Laren mention them. Certainly some people who felt especially hard done by the occupation might question where their gods were during the suffering.