I think that the problem isn't necessarily that DF is difficult to understand; the interface is reasonably well-organized except for some directional input woes (and, of course, the military screen, though I think that much of its bad reputation is a legacy of 31.01, where it was so buggy that you honestly couldn't tell which problems were your fault and which were the game's) and most tasks are fairly simple to carry out.
The problem is that DF is ridiculously hard to figure out for yourself because there's nothing else quite like it. When you get the latest Zelda, Elder Scrolls, Dragon Quest, or cheap CoD knockoff, you already have a pretty good idea of what you're supposed to do and how you can do it, based on previous experiences with games of that type. With DF, however, you have absolutely no starting point; instead of just skimming the instructions to see what's different, a new DF player has to completely learn a new way of playing a game entirely from scratch.
This is helped not at all by the fact that there really is a lot to do in DF, and that quite a bit of it urgently needs doing. You NEED to learn RIGHT AWAY how to get food, booze, shelter, defenses, and so on or else your fortress won't make it past the year; this, I think, is where the fabled "learning cliff" originates -- it's not a particularly high cliff, but it must be climbed immediately with all haste and the slightest misstep leaves you back at square one.
The sheer scale of DF can also be a little hard for a newbie to grasp (and holy wow, that statement seems condescending). It's easy to mistakenly assume that you've already learned everything important about the game, only to be bit in the ass by some important detail that you weren't aware of and honestly had little reason to expect ("What? Adamantine warhammers are actually a terrible idea? Crap." "What? This game simulates hydrostatic water pressure? Crap!" "What? This game models realistic melting points for each material and just being made of stone/metal doesn't mean a floodgate will hold up in high temperatures? CRAP.").
EDIT: Fixed errant commas.