The uncertainty occurs when a reader (or an audience) reads a story and dislikes it. When readers dislike a story, they can dislike it IMMENSELY. Remember, people, that fictional authors have gotten arrested or threatened (like Salman Rushdie) for WRITING something, not for having committed murder or thievery. Not because the story is bad necessarily, as we all know from Banned Books Week and the charges of witchcraft against Harry Potter, but because the story offended the reader. It may be a case of bad timing, like a cartoon with severed heads after some terrorists have performed a public beheading (which happened twice to Stephen Pastis, the cartoonist for Pearls Before Swine), or it may be a case of the literature being written in a time when marital rape was not a crime, like in Gone With the Wind.
You cannot control this. You cannot help if other people find your book offensive; take their criticisms with a grain of salt and think about them. I scrapped a whole comic storyline (about four strips) because four people said the joke was offensive; while I'm glad I never did it for different reasons, it killed me that I had offended a group that I respect. I know how that feels, being accidentally offensive, but if your story is clear enough, at least one or two readers will get the point.
You owe the readers a good story. Period. Characters they can follow, a plausible plot-line or storyline, and a fantastic ending. Readers will feel cheated if you resurrect the dead without a plausible explanation. They will dislike villains that pose no threat, or a one-sided perspective of a romantic relationship. They will feel cheated if you give a happy ending that the protagonist does not deserve; the same goes for the tragic ending that results from ultimate failure. And if they don't get the joke, or the riddle that you didn't mean to insert, then you are going to have frustrated readers.
So don't despair if a hater calls you a fascist, or threatens you; and don't despair if they catch errors in your story. In class, people liked my story, but they wanted to know who the mysterious creature was that helped the protagonist. I'm still stinging, but I can fix it. You can fix you story, so don't get in a funk.
So remember: courtesy to yourself, your characters, and your readers. But also: You. Can. Fix. Period.