1) Phrasing: if the person commenting uses only cliched terms to criticize your characterization, the comments are useless even if there's a flaw on your characterization. "Cardboard characters" simply means the commenter wasn't convinced by, engaged by, your characters. This could be a limitation in that reader (there are incompetent readers, and most of them think they're good readers), or the reader didn't like the characters for other reasons (confuses "familiar character type" with "shallow"), etc.
2) Experience outside literature: does the person commenting have enough knowledge and experience to know when you got the behavior right? For instance, I've written characters that felt real to people who had experience in that field, but were questioned sharply by those without any such experience. Even though the reader lacks experience, the best writers can convey enough of an unfamiliar setting/occupation so that most (never all) readers will accept the reality...but not if the reader has strong and unrealistic biases in place. A common flaw here is that a reader has a theory of character (of human nature, of social/cultural reality) that is not based on fact, and thus imposes a false standard. I remember shocking a child from a very strict religion by not having the behaviors she was sure all non-members of that church had. I've run into readers/reviewers/critics who had just as unrealistic beliefs about genders, religions, occupations, political viewpoints, etc.
3) Experience with literature: Does the reader have the reading skills to recognize the actual characterization, or is he/she confined to a theoretical or fashionable approach? Most writers have had reviews that made them go "Huh? This person could not have read MY book!" Some readers, though possessed of basic reading skills, are hasty in judgment and do not read books thoroughly even if they finish them. They do not know how to read deeply, how to notice subtlety, how to recognize deeply layered characterization. Again, unrealistic literary theories create some of this problem. If a reader believes that stories are binary--either character-driven or plot-driven, and that plots in which something happens necessarily means that characters lack complexity and depth, they will not see what's clear to more perceptive readers. Reading skill takes time to develop, and it also takes the ability and willingness to read the book that's there on its own--and compare it to reality beyond books--rather than try to fit the book to an existing category.
Which boils down to: most of the criticism of characterization I've seen is way off base.
That does not mean it's useless to the writer.
It's a matter of proportion. If the readers who think your characters are boring, shallow, or just plain wrong constitute 5% of the responses, then you've just run into the reality that no book satisfies everyone. If half the readers don't like your characters, you have a problem, but it's probably not exactly what you're hearing. If the readers are people you know (your alpha readers) you can train them to give you useful feedback; otherwise you have to look at your characters again and rethink what you know about them and what you've actually shown. (Another post will deal with training your alpha/beta readers so they're the most help.)
Some writers and a minority of readers like to use unlikeable characters. If you've chosen to write about unlikeable characters, then you can expect that a lot of people won't like them, and won't like your story as a result. Your choice--you can accept that you're writing for a smaller audience, or you can modify your characters a little, give them a redeeming trait that may attract some more readers.
If your characters are intended to be likeable, are they likeable the right way? Or did you give them the kind of flaw that is really annoying all the way through, rather than plot-critical in a few places? Do you and most people agree on what likeable is? (Novice writers may use theoretical versions of likeable rather than real-world likeable...may use Sunday School niceness and perfect manners instead of genuine warmth, wit, etc.) Are they too good, too perfect? Are they not good enough?
Have you shown your character's weaknesses in a way that a) will be recognized and b) will be accepted by readers--so they can empathize? Have you shown your character's insides--his/her feelings about that weakness--as well as the effects of it?
If your characters lean toward the ordinary, have you put hooks to their potential interesting/extraordinary bits in a way that most readers will notice them? Did you make clear connections from their innate and acquired traits, via their motivations, to their actions? That is, is the chain of causation connected all the way through from biology and psychology to action and consequences?
If you conceive of characters in depth, if you know their insides intimately, you can still leave out (because you know so much) something that's essential for readers--even the best readers--to grasp if they're going to commit to the character. Though you can ignore the snarky, dismissive comments to some degree, it's always worth checking to see if you *did* leave out what you meant to put in, or if you added details that confuses/camouflages the real nature of your characters.