Gersen: The problem is when some peoples starts analyzing everything you write and start finding political statement in everything, and start attributing your characters/world actions or belief to yourself.
It really doesn't work like that. This is not analysis. Good history novels usually reflect the prejudices of their times, with, ideally, protagonists being understandably prisoner of them (to some extent, because every historical society also had its own inner critics). But there's a difference between showing and glorifying, even between explaining, excusing and justifying. A difference between describing a character (or society) and describing the objective realities of the world. A character or society can be described as believing that all jews/blacks/homosexuals are subhumans, or jews/blacks/homosexuals can be described as subhumans. Inbetween, you can have descriptive discourses that are framed as insightful (epic speeches of the flawless hero, badass sarcasm of super ownage, etc) or flawed (contradicted by the background world, validly questionned by other characters, doubt cast by the protagonists' known flaws, etc) or part of an evolution ark, etc. The fallacy is in the lowbrow assumption that meaning can be derived from isolated elements. It's the system that matters, in communication.
And more than a fallacy, it's a rhetorical tool, used with false outrage by racists who point out "double standards" of the form "hey, their character is allowed to say this, but when ours say the same thing we're racist ?". The answer being "their character is presented as being wrong, yours is presented as being right". And this stems from the work as a whole.
As for the pandering thing, also pointed out by Rjbuffchix, it's very subjective. Firstly because nothing is universally obvious or universally established in our globalized world (I used to have very little patience in front of productions with heavy-handed obvious moral discourses, but since then I've measured -including on these very boards- how little this supposed basics are shared). Secondly because the very reason why some values seem subculturally obvious is precisely that they keep being hammered by such unsubtle stories (starting with childhood tales and mythologies). Thirdly because, as I said, a discourse is all the more salient as it contrasts with your own views, so what is "pandering" to some may often be "neutral" to others : see how shocking it gets to conservative when a franchise starts featuring female, black or homosexual protagonists. It's seen as "a thing" (in contrast with normality), while the "thing" for the authors would be an all-white all-male cast (and diversity seems more natural in contrast). "Pandering" is a questionable notion. Not to mention all the "pandering" that would then apply to the glorification of consensual values, everytime the baddie is presented as a baddie for transgressing other taboos (murder, theft, regicide, rape, etc). Many values others (and even more "already agreed upon") than antiracism get openly encouraged in our tales, by the hero's qualities or the plot's antagonisms. By the "pandering" logic, these would sound all the more redundant, useless, cheap and easy ("oh, yet again the so-called baddie wants to dominate the planet ? we get it we get it, dominating the planet is bad, sheesh"). But paradoxically, the least consensual the theme, the more it's deemed "pandering", and "preaching the obvious". Again, because visibility.