What I meant was that science has proceeded with minds that constantly questioned the prevailing religious orthodoxy. It took the Catholic church 500 years to finally, formally acknowledge that Galileo was right. He dared go against the church's teaching that the Sun revolved around the Earth. He wasn't an atheist (but few were yet in the 16th century).

You (probably) don't believe in 99.99% of the gods that humanity once believed in. We differ by only .001% in this regard.