Ryan Britt has a very good post at Tor.com entitled “Genre in the Mainstream: Does SFF Marginalize Characters?” It's well worth your time.
Britt hits on a good point when he remarks that a typical science fiction book simply has more things competing with the characters for attention than a more conventional story- a character who might seem perfectly acceptable in isolation may seem lackluster when placed alongside ideas that are much more interesting than he is. In a somewhat similar vein I would add another factor, the inescapable scarcity of resources that go into a book's creation.
Time is finite, energy is finite, and the number of words in a book is finite. Provided with equal amounts of these resources, “serious” fiction can put more into its characters because it generally does not place a significant focus on subject matter other than the characters; the plot and setting are mostly or entirely there to further characterization or theme, rather than as things meant to be interesting in themselves. Character-focused fiction is usually also free from the need to explain the nature of its setting or the laws that govern it.
Often, science fiction simply does not have the resources to spare. Take a book I reviewed here a while ago, Incandescence by Greg Egan. Not a character piece, to put it mildly. Its length is modest, 256 pages in the Night Shade Books copy that I own. Now, there are probably ways it could be tweaked to make the characterization somewhat better while staying at that length and without any damage to the book's specifically science fictiony virtues. But probably not by much, because our hypothetical Incandescence 2.0 also still needs to cover, with same amount of detail and clarity of explanation:
A galaxy-wide multi-species civilization. Ways in which uploaded personalities originating from biological species with radically different physiologies, psychologies, sensory organs, etc. interact comfortably in shared virtual environments. A mysterious, isolationist second civilization in the galactic core. The workings of a galaxy-wide communications network that is limited to light-speed transmissions and carries not only messages but entire machine intelligences. Panspermia. The physics of space close to black holes. The physics of space close to black holes. The biology and society of an alien species. The invention of the scientific method by a member of that species, and the gradual process of discovery through experimentation. The consequences of living in an environment where the effects of relativity are significant enough to be noticeable in day-to-day life.
And so on. And then there's the actual plot that still needs to fit, too.
Some writers are better than others at creating strong characters while still giving attention to plot, setting, and ideas. But there are still trade-offs to be made and different authors will tend to be more effective at some ratios of these elements than others.
Obviously, better characterization is better than worse, all else being equal. Some of my favorite science fiction stories are strongly character-based. But- as Britt alludes to- much of the criticism leveled at science fiction on this matter is built on the assumption, often the explicit assumption, that the emotions and personalities of the characters is what fiction is really about, or at least what it ought to be about. It's not surprising that this would be so; in people, being strongly socially and emotionally attuned is a much higher-status trait than the sort of attributes that often draw people to science fiction, and it makes sense that the status of science fiction would correspond to that of the sort of personality it brings to mind.
Which is why, ultimately, my answer to the question “Does SFF Marginalize Characters?” is, “Frequently, yes. So what?” One of the things I love most about science fiction is precisely that it treats things like science, technology, and carefully thinking about how systems work and how they might be affected by change as actually interesting, instead of being bound by the sort of assumptions that privilege one facet of the human mind above all others as the one stories should be about.