... "sympathetic" isn't the same thing as "compelling" — a character can be unsympathetic but utterly fascinating and spellbinding. Like a lot of the things on this list, this is all in the execution — if you're going to go with a protagonist who's fundamentally unsympathetic or unrelatable, you're going to have to do an amazing job of making the reader care about him or her in spite of everything.
The Stars My Destination comes to mind as a great example of this. Gully Foyle, the hero — er, protagonist -- is one of the less likable characters of any SF story I've read. What makes him the center of such a compulsively readable story is a) we know exactly what he wants, but we never know how he's going to go about trying to get it next, and b) he does humanize as the story goes on. He begins as a brute, mutates into a creature of revenge, evolves into a spy / supersoldier, and ends as a repentant and a transcender of human limitations.
Yes, it's The Count of Monte Cristo rewritten as SF, but no one minded. (Certainly not me.) The rewrite was so stylish and loaded with so many ideas that have not only endured but gained relevance with time that it's hard to complain. But on the whole, Destination is the exception in more ways than one. Two, actually.
The first problem is something I have groused about a great deal: the way SF all too often becomes about an idea, a concept, a situation or a punctuated equilibrium rather than a person. It might be easy to say that's what SF is -- it's "a literature of change driven by technology", and so the people are gonna get at least some short shrift because of that. But that all too easily turns into either an excuse to ignore character development entirely or a backhanded way to forgive a writer who's simply not very good at doing such things. I would gladly take dimes for every single instance where I've been told "Well, _____ is not great when writing about people, but his ideas are awesome!"; I'd have enough dimes to pay off my mortgage twice over. (Isaac Asimov is often cited as one such author, but frankly Asimov's handling of character, rudimentary as it can be, is a lot better than some of the other stuff I've seen.)
The second problem is an outgrowth of the first, and this is where I go from Observation into Soapbox. Any literature that develops a built-in excuse to not be great with character will eventually develop that many more excuses to not be great with character. People read books, and if we don't see at least a little of ourselves reflected well in the books we read we're going to feel that much less satisfied. And, worse yet, maybe never quite knowing why.
On a side note, the whole concept that a protagonist doesn't have to be sympathetic was essentially demolished with the popularity of A Game of Thrones. The new problem seems to be writing a sympathetic character without making him seem like a sissy who'd be eaten in his sleep by the Starks. That said, I'm of the opinion Gully Foyle would make the Starks look like pikers on a camping trip. Here is, after all, a guy who is trying to extract information from a man who may die from a coronary — and Gully's approach is to cut his heart out and put him on life support.
Other Lives Of The Mind