Did Christian church find it difficult to accept Nicolaus Copernicus' heliocentric theory?

Copernicus himself did not attract much attention from Church authorities. However, his theory did, after his death. Copernicus theorized that the planets revolve around the sun and the Earth rotates on its axis to produce day and night. This was thought to contradict the account in Genesis. The vision of Gen. 1 states that the earth existed prior to the sun, and that God created day and night prior to the sun, moon and stars.

In the beginning God created the heavens and the earth. The earth was without form and void... And God said, “Let there be light”; and there was light. And God saw that the light was good; and God separated the light from the darkness. God called the light Day, and the darkness he called Night. And there was evening and there was morning, one day... And God said, “Let the earth put forth vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, upon the earth.” And it was so... And there was evening and there was morning, a third day... And God made the two great lights, the greater light to rule the day, and the lesser light to rule the night; he made the stars also... And there was evening and there was morning, a fourth day.

So in Genesis, the earth already exists in the beginning, although it is without form at this point. Day and night are brought into being on the first day. Trees and other vegetation are brought forth by the third day. It is only on the fourth day that God places a greater light in the sky to rule the day (the sun) and a lesser light to rule the night (moon).

Copernicus himself did not attract great opposition from the Church until after his death. A half-century later, experiments by Galileo in 1609-1612 with the newly invented telescope attracted more attention. His claims resulted in serious opposition from Christian authorities, until further advancements in scientific technology led to the acceptance of the heliocentric view.

If the earth's rotation is what causes day and night, then the literal reading Genesis account would be overthrown. Similarly if the earth revolves around the sun, then God would have created the sun prior to the earth. We today usually do not take this part of the Genesis literally since the Copernican view was ultimately accepted. But in the 17th century, when Galileo's work attracted wide attention, the theory was highly controversial.

Because Copernicus was wrong. It's really as simple as that.

Yes, he put the Sun in the right place, but there's more to a solar model than just the central point, and on virtually every other detail, Copernicus's model was not only wrong, it was even worse than existing geocentric models. The astronomer who produced an accurate model of the solar system was not Copernicus at all, but Kepler, working approximately 60 years later.

The principal difference was, Copernicus was constrained by Platonic mysticism, trying to shoehorn planetary orbits into perfect circles when they clearly didn't fit and piling a big mess of epicycles on top of them to force his preferred model into conformity with the data. Meanwhile, Kepler looked at what the data told him and realized that this actually fits, and quite cleanly too, if instead of perfect circles the orbits are ellipses with the sun at one of the focal points. (In other words, actual science.)

In the Legend, the conflict was between Science and Religion. But in the History, the conflict was between two groups of scientists, with churchmen lined up on all sides. Copernicanism was supported by humanist literati and opposed by Aristotelian physicists; so it was a mixed bag all around. Science does not take place in a bubble. International and domestic politics and individual personalities roil the pot as well. The mystery is not why Galileo failed to triumph – he didn’t have good evidence, made enemies of his friends, and stepped into a political minefield. The real mystery is why Kepler, who actually had the correct solution, constantly flew under the radar. A deviant Lutheran working in a Catholic monarchy, he pushed Copernicanism as strongly as Galileo; but no one hassled him over it. Too bad he couldn’t write his way out of a paper bag.

-- The Great Ptolemaic Smackdown, an excellent series of articles that discusses this issue in depth

There are 2 reasons why Church leaders at the times of Galileo and Copernicus did not accept their theories. The first was that it contradicted many theologians' and philosophers' understanding of Genesis. Of course, it also did not contradict many other theologians' and philosophers' understanding of Genesis (one notable example would be Augustine, whose exegesis of the early chapters of Genesis does not conflict with heliocentrism).

The second reason is that Galileo, working from Copernicus' ideas, was not actually able to prove his theory. He needed to observe something called the Stellar Parallax, and telescopes capable of observing this phenomenon would not exist until between one and two centuries after his death. Because he was teaching a view that fundamentally contradicted the received wisdom of the era, he was told that he would need to prove his theories if he wanted to keep teaching them. Since he was unable to prove them, he was ordered to stop teaching them.

With Galileo in particular, there were also political elements at play. He made himself an antagonist against the Pope, so it should not be surprising that the Pope, a fallen human being, retaliated. The Pope simply used the fact that Galileo obstinately refused to recant his (at the time) unproven theory against him.