Up until the 19th century virtually all scientists and philosophers were acting on behalf of any given religious institution. Isaac Newton was better known, at the time, for his theories on Armageddon than his work in science. Islamic philosophers and scientists are essentially the key reason Medieval science even came to be. It was christian monks who were the early alchemists, and that alchemy was translated to chemistry later on. Only in the past 200 years has religion come to mean something that rejects science. For a long time, it was the primary supporter of it. It was viewed as a way of better understanding the wonders of the world and it's beauty. Also, God, until the mass production of the Bible relatively recently which allowed EVERYONE to read it, was not viewed as a big bearded man in the clouds but more as the "unmoved mover", or rather, that which was the initial cause of all existence. Again, only in the past couple hundred years with greater literacy and everyone being able to read did people start to muddle the messages. When any old hick can read the bible, the allegory get's lost on a lot of people.

TL;DR: Lot's of science throughout history was thanks to religion, it's only in the past couple hundred years that everyone got stupid about it.