I take pride in writing fantasies that can be read on several levels. If you look, there is more there than just a great (I hope) story.
So what do I do when I see a reader's comment that says something like, "A good entertaining story, but no great depth"? Get all huffy and mutter about readers that can't see past the drip on the end of their noses?
And what about the opposite: the reader who talks about the deep dark meaning of my work and how I have commented on the connections between Donald Rumsfeld, the Da Vinci Code and the melting of the icecaps? (And no; no such book or reader exists...yet.)
Once a writer's work gets out there into the public domain, what happens to it is largely beyond their control. And no matter how a reader might have mangled the subtler meaning, the writer has to grin and bear it - and to a degree sometimes even take the blame. Perhaps your writing lacked the clarity you thought it had?
Mostly though, I don't think that's the point. Each reader takes something different from a writer's work. Perhaps the book did no more than entertain them for an hour or two. Perhaps it made them think about deeper issues of morality and ethics. Maybe it made them re-examine their politics, their environmental concerns, their relationship with their significant other, or how they feel about their dog. Perhaps it made them happier. Perhaps it even inspired them. And the writer will never know these things unless the reader sends an email or a letter or writes a review.
What does matter is this:
The writer has tried to let others see the world through the lens of his own eye. Each writer brings his own joys/fears/politics/ethics/morality to his writing. If, for a moment in time, the reader has been transported somewhere else, to see ( figuratively or literally) something they would not have seen otherwise, then the writer has done part of his job. If the picture the reader sees is not quite the one that you the writer intended, well - at least you have made them think. And that can never be a bad thing.
So if the reader doesn't "get" what I have written, I smile, maybe learn something, and move on. I'm just glad there are people out there who read my work.