If anything, using don't / can't with "understand" has a very subtle difference that sometimes might be no difference at all. The use of one over the other might depend on context, or personal preference.
I don't understand you.
I would use this if I was able to hear the words you are saying, but I could not understand the context or the overall sense of what you were trying to say.
I can't understand you
I would use this if I am unable to distinguish the words you are saying, or if the entire sentence made no sense at all.
As an example, suppose I'm on the phone with company's customer service and something is wrong with their phone so that their words are garbled. Then I might say,
"I'm sorry, I can't understand you, could you please say it again?"
On the other hand, imagine the same phone call and the person on the phone is explaining some complicated reason why I can't get what I want. Then I might say
"I'm sorry, I don't understand what you mean, could you please explain in a different way?"
However, this is not universal. Some people may say don't when I would say can't, and vice-versa.