The conflict between religion and science slowly emerged in the 17th-plus century, and really took off in the 19th with Charles Darwin, because evolution flat out contradicts creation. It was the icing on a cake that had been brewing for a while, but it wasn't always so.
Throughout the middle ages, monks were the scientists of their time, conducting experiments and exchanging theories all over Europe. In fact, the word "scientist" was invented in the 18th century. And there was progress in the middle ages, as Technology 500 AD shows.

In our time period, even this was in the future. Science is of little importance to people barely surviving.
Nevertheless, we often have a wrong picture about these times, thinking times were worse and people more stupid than they really were. For example, people didn't think the Earth was flat - no, they didn't. We have religious scholars clearly speaking about a round Earth and a globe.

People did understand the world they lived in quite well. Their knowledge differed from ours due to the circumstances they found themselves in. We today learn how to use computers and drive cars. People in 500 AD would know all the plants and animals in their area, they would know a craft or two, and in fact due to the absence of writing would have developed much better memory than most of us today have. You have heard of the Illiad and the tale of Odysseus, probably. Today's print editions of these two have over 700 pages and together they are about 180,000 words long. These works were transmitted orally. Singers, because yes, they were generally sung, would know them by heart.