Basically what it boils down to is power and religion's (religions with a central focus on god) inability to change through the times. Religion has always had this struggle for power whether it was against the church, starting with Charlemagne, or against science, starting more recently since the Renasaince.

It doesn't stem from Theocracy, when religion was used to as a means to govern people. To my knowledge that was never really a strong governmental model in Europe. Sure there have been influences such as a the Mandate of Heaven, Devine Right of Kings, centralizing countries, or used it as sort of a model. However, there has always been a power struggle between the church and state that has just kept getting worse and worse. Most notable start was when King Charlemagne was deemed the king of the Holy Roman Empire by the pope, and his retaliation was deeming the Pope the pope. The issue ceased slightly during the Medieval times. During that time religion was the only hope for the people. It didn't stop completely though. In the last crusade, some Kings banded together to prove their loyalty to god. They succeeded, but the ruler they were saving had a heart attack and in frustration they pillaged the very kingdom they were suppose to save and raped all the women.

Getting out of the Medieval times and into the Renasaince, the model shifted from the man and his relations to god to the man and how he may contribute to society. Around the same era, you have people starting to question authority. John Calvin provoked people's thoughts so much that he uninentionally made a new religion, and Martin Luther's exile and led to more questioning forming a new church. Then there was King Henry VIII's issue with his wives. The church was being undermined on every front at this point.

Literature didn't help this situation out at all. As science progressed, literature conjured up horror stories of humans tampering with nature; creating freaks such as Dr. Jekyll and Mr. Hyde or Frankenstein.

On the extreme ends, the church really set itself up for its own faults by its own shiftlessness. While the times changed, the church MUST stay constant. You cannot simply say a supreme being exists, get proven wrong, and then say while it was wrong, it's still a supreme being.

In a more practical sense, science and god can, and does, co-exist. Majority of the world believe in a god, yet we still try to progress in science. But that comes from the basis of religion, which is faith.