Understanding Human Consciousness
It is not just the brain itself that makes understanding human consciousness difficult. Similar to how many people find it difficult to accept that there are no such things as ghosts (particularly when alone at midnight in a creepy graveyard), people, in general, may also find it difficult to accept human consciousness for what it really is.
The human brain has been programmed to distinguish life, especially conscious life, from other functioning systems. There is a good reason for this distinction: it has been a critical factor in our evolution. For example, you don't have to worry about angering a dust devil, but you do a bear. It may be easy to sneak up on a small waterfall but not on a rabbit. Dealing with living things involves special considerations that are simply not present when dealing with other functioning systems.
However, since living things are, in fact, functioning systems, the distinction between these two classifications can sometimes become unclear. Dogs appear to identify functioning vacuum cleaners as living things. We humans make anthropomorphic interpretations of complex functioning systems--of ships, airplanes, cars, and computers. In the past, such interpretations were even more prevalent--of weather conditions, ocean conditions, celestial bodies, etc.
Distinguishing life from other functioning systems has also helped people adopt a special view of themselves. Deeply strengthened by the obvious capabilities of humans over those of other living things, this special view of humans has helped people believe in human connections to supernatural beings, reincarnation, and spirits.
Accepting such beliefs has been very important in the recent evolution of humans. Indeed, when religious war or intolerance broke out, a person who was of the wrong religion, or who was not successfully assimilated into the new one, could be killed. In many cases, just not believing in certain particulars of a prevailing religion--regardless of how based on reality those particulars were--could get an individual excommunicated, imprisoned, tortured, and/or killed. Such direct manipulations of human populations have been significant evolutionary factors.
Hence, these factors may be the deepest reason why it is against many people's innate (evolutionary and social) programming to recognize each of us as a complex physical system and our consciousness as just a functioning of that system. However, to recognize ourselves for what we really are, I believe, is much more valuable in the long run than appeasing intuitions that support scientifically unfounded constructions.