I think there are three major reasons why a lot of people have trouble accepting biological evolution:
- We humans aren't very well equipped to understand the vast spans of time involved in evolutionary (or, for that matter, geological) processes. Yes, it is unintuitive for complex organisms to evolve, but when a one-hour morning meeting seems like a long time, it's not surprising that we can't instictively grasp a hundred thousand or a million or 65 million years. It also explains why so many people don't think climate change is happening, even though it's only on the scale of decades. Inconvenient truths are easier to ignore when they don't fit with our day-to-day time scales.
- Most of us don't understand how the scientific process works. That's fine when the subject is uncontroversial: no one is arguing againt the fundamentals of what science has learned about gravity, or electricity, or the process of photosynthesis. Even continental drift, which seemed like a crazy idea when first proposed, turns out to be true, and those who argue against it today seem like crackpots. But start bringing religious or odd new-age dogma into it, and it's not hard to obfuscate and misrepresent the science (even unintentionally) to make it seem like facts really aren't, and to fit better the way we'd prefer things to be.
- We're afraid to die, especially if it means that we really die, i.e. once our bodies stop working, we as individuals cease to exist, so that there is no life after death. Personally, that's what I think, and I've come to be comfortable with it. But many (maybe most) people aren't, so we want there to be an afterlife, and with that comes the ideas of spirits and gods and heaven and—well, once you get there, it's not that big a leap to having someone or something create and guide life on earth too. Certainly you can accept both evolution and the afterlife, and plenty of people do. But I also think it is, once again, intellectually inconvenient to have whole realms of philosophy beyond physical life, and then leave every living thing we can see be subject to something as non-metaphysical as natural selection.
Note that these problems have little to do with how the world really is. Just as the world was round and went around the sun even when we thought it didn't—and did so even before there was anyone or anything to ask the question—and just as our brains controlled our bodies even when we thought our hearts did, it's clear that life (including us) has evolved, and continues to. What's new is that only in the most recent epoch has that process created minds that can understand the process, or misunderstand it.