The simple truth
Common conception has it that it's the complex things that make us stumble. And to a certain extent this is true. Systems that are simpler are easier to understand and modify than systems that are complex. Complex subjects give us a harder time than simple subjects - people who want it easy study "soft" subjects like psychology, not demanding subjects like quantum mechanics. As they say, "the devil is in the details".
But I don't think this principle applies to philosophy or worldviews. Here, it is the simple truths that are most difficult to grasp and make us stumble, not the complex ones.
Look at Creationist rhetoric, for example. Creationists are not Creationists because they object to, say, Neo-Darwinist ideas on the evolution of the horse, or whether the bones in the human ear really evolved from the reptilian jaw. While they may use these elements as part of their examples, that's not why they are Creationists. They are Creationists because they are firmly entrenched in the Christian worldview, which preaches that man is "special" and "superior", and cannot accept the simple truth that man is an animal. They also cannot accept a mechanistic account of life, which excludes the teleology of their choice. Neo-Darwinism is supremely annoying for the teleology fan.
Likewise, crackpots often argue against Einstein and the Theory of Relativity (which, as I mention on my Insolitology FAQ, is their first pet peeve - the second being homosexuals) - not because of any specific equation or concept, but because they cannot accept the simple truth that there is no privileged frame of reference. Once again, the Theory of Relativity supremely annoys their belief that the human experience is "special" in the universe, and that the universe can somehow accomodate them as absolutes.
Quantum mechanics is hard to understand mainly because it's completely counter-intuitive to our daily experience, not only because it's complex. A complex but intuitive topic is just a matter of effort. A counter-intuitive topic, on the other hand, will stump most people regardless of its complexity.
Simple truths in philosophy are counter-intuitive for most people. That's fine. But the fact that they are simple should bolster our confidence. We must confront them bravely, evaluate them on the basis of the evidence, and not shy away from the consequences either way. Of course, simplicity should not be seen as the mark of truth. Lies are also simple, for the good reason that they don't need to account for the facts, and simplicity has a lot of emotional appeal.
Some fashionable simple propositions are dead wrong, but are seductive because of their simplicity. One such proposition is : "morality is just a social construct". Like most lies, it is simple, attractive, and wrong. The fact that it is monstruous and repugnant is only a consequence of this falsity.
How do you make the difference between simple truths and simple lies ? By checking their premises, and the worldview they belong to. A proposition like "morality is just a social construct" belongs to nihilistic, inter-subjectivist worldviews like utilitarianism, New Age beliefs and post-modernism. These worldviews are wrong because reality is not an inter-subjective construct, and neither does it care to accomodate people's beliefs. Reality works according to well-defined natural laws. Therefore we can reject such a proposition.
Of course, you can also make an argument from the fact that science works and that moral principles work, but that would beg the question of standards for "working". Outside of rational worldviews there's no reason to accept the standard of, say, "predictive power" that is used in science. This is why worldviews are so fundamental. They are also fundamental in the sense that simple truths are more often than not puzzling because you don't have the correct worldview to understand them.
Take the truth that "man is an animal". If you come from the Christian worldview, you can't possibly accept this as true. The whole point of Christianity is that man is "special" - man has a "soul", man is in relation with God, man can be saved, man has a purpose. So how can man "just" be an animal ? This seems as incongruous and absurd as the idea of a "soul" is to me. I equally can't possibly understand why anyone would want to claim to have a "soul".
Or take the other simple truth that "people are generally nice". Christianity tells us that man suffers from original sin and is depraved without Christian doctrine. Many Christians still accept this as true, and see anyone but them as morally flawed. So Christian doctrine must be preached and imposed on others in order to make "a better society". If you tell a Christian that people are generally nice, he'll answer you "that's your opinion, BUT...". Then they will talk to you about the news or about some bad event that happened to them ten years ago.
Another area of simple truth is morality. Propositions such as "belief is evil", "religion is evil", "religion is morally irresponsible", "war is evil" or "murder [viz capital punishment] is evil" are simple and true but unlikely to be widely accepted. People will agree or remain indifferent to a more abstract principle such as "non-coercion is virtuous", because the concept "non-coercion" is not concrete enough for them to understand. But ask them if war is evil and they'll talk your ear off.
The simple truths of the emergentist worldview - Naturalism, Materialism, Reductionism, Determinism (or as I like to call it, NaMaRD) - are those that give the most trouble to our opponents. From their perspective, their lack of understanding about order, it is easy to see why they would consider such truths to be absurd or lacking. However, if we did a comparison with other worldviews, such as the simple truths of the Christian worldview, we would find them equally lacking.
In the end, as I said before, comparing a premise like "everything is material" with a premise like "God created the universe" presupposes a worldview with relevant standards of judgment. If anything, I would say that the way you react to the basic premises of different worldviews shows where your heart is. If you claim to be an individualist, say, but feel great affinity for a premise like "people are too egoist and should conform to the common good", I don't think you should call yourself an individualist. But that's another issue entirely.