Many religious people have no problem accepting the theory of evolution as being the way that God made the variety of animals and plants that we see around us today. Kenneth Miller, a noted defender of evolution and a staunch Roman Catholic, explains that there can be only one truth, and that faith and reason must both point towards the same truth. If the two are starkly at odds with each other, then something is wrong. Given the huge amount of evidence supporting evolution, evolution most probably is true: therefore God must use evolution as His means of generating the awesome variety of life that we see on earth today. Theistic evolutionists like Dr Miller therefore have no trouble accepting that humans are in fact related to chimpanzees; that humans are in fact apes.
The trouble starts, as I see it, when a small subset of Christians, called creationists, apply an over literal filter to the Bible (other religions are guilty of this too, and have their own fundamentalists). Genesis 2:7 states "And the LORD God formed man of the dust of the ground..." Therefore this becomes the only possible truth. Anything that says otherwise must simply be wrong. Creationist websites such as Answers in Genesis state that God created discrete kinds ape kinds, fish kinds, cow kinds etc and the human kind. A cow kind cannot become a fish kind. An ape kind cannot become a human kind.
Creationists demand a literal interpretation of Genesis that is incompatible with reason. But it is not just creationists who believe that God gave humans and only humans a soul. Genesis 2:7 continues "and breathed into his nostrils the breath of life; and man became a living soul." Humans are not simply created separately; we are special. God breathed a soul into us, and not into the animals.
The second part of the Genesis quote, I think, makes it harder to reconcile special creation with evolution. Most Christians are, I think, soul-believing non-creationist types. But exactly when and where, in the continuous progression from chimpanzee-like ape to human, did we propose that get imparted with a soul? Did Homo habilis have a soul? Were Neanderthals part of God's special creation too, with souls, or were they just animals like chimpanzees? Such questions are not easy to answer. Souls do not fossilize. Souls have no genetic component that can be traced through DNA analysis. This makes evolution a tricky concept even for regular Christians. Life, according to evolution, is a continuous process, with small gradations from one species to another. So did souls evolve along with us? Or was there some point at which God decided that humans were ready, and gave us souls? If so, does this mean that humans are now not part of nature: that we can no longer evolve?
So, even for your average, run-of-the-mill Christian, evolution throws up problems. I'm not sure how Kenneth Miller answers this question. But I think that for many, the easiest solution is to ignore it and simply deny that we really are evolved from apes.