One of the first things I learned in composition class was the importance of taking responsibility for the clarity of my writing. OK, maybe that wasn't the first thing, but I do remember being taught that it is not the reader's fault if my writing is misunderstood.
So I get really cranky when I'm reading a blog or message board and someone responds to a comment with "you misunderstood!"
No, they didn't. Or maybe they did. Either way, it is the responsibility of the writer to clarify. The proper response to a misunderstanding is, "I'm sorry, I was unclear. What I meant was..." Yes, even if the writer knows he or she was clear. Even if the reader made it obvious that he or she misread or misunderstood the post/comment/whatever.
Responding in any other way is like saying to the reader "your reading comprehension skills are poor." Or even "you are too stupid to understand."
Misunderstanding are inevitable, you say? Yes, that's true. Still, take responsibility for misunderstandings. People will appreciate the way you communicate with them.