This expression seems to be used even when the speaker does not expect the other person to agree with them.
What would the intention of the speaker be? Is the expression considered rude?
As well as the uses already given, it can serve to fill out an excuse, usually with 'you'll' rather than just 'you'. For example, 'I'd love to come, but that's the day I'm having my etchings framed. I'm sure you'll understand.'
I have often used the term in order to be polite and not patronise the listener. I have used in a context of not needing to explain a series of thoughts and almost used it as "assumed knowledge" for the listener. So for example
We have to ensure that those goods are sent out this week or else we start to get complaints and financial penalties. I am sure you understand.
Rather than explain in detail which customers will complain and the associated financial penalties, the phrase has been used to bypass that explanation and just acts to reinforce a sense of assumed knowledge of what may happen.
In another example, it can be used to explicitly avoid part of a conversation. So the example this time may go something like:
I wanted to attend the wedding, and I was pleased that she found her perfect partner, but given we dated a few years ago and I still have feelings for her. Well, I am sure you understand.
I can think of examples also where it could be used aggressively, passively, encouragingly and so on. But each example indicates the listener has assumed knowledge of the implication.
I don't think it's considered as an expression. It's plain English and implies that the person you are speaking with already knows what you will say. I dont think it's rude unless you shout at the guy; or put it in a context that makes it rude. For example:
Hello, Dave. How are you?
Hey, Mike. I am good. What's up, buddy?
Well, I am sure you understand this (I am sure you know this) but I am going to tell you anyway...
I am sure you understand this... [But I am going to repeat it to you because you are a moron...]