Not especially. Face-to-face, I could sooner imagine somebody asking "do you hear me" in a demanding, or even threatening (or simply rhetorical) way for emphasis. But of course nobody should read too much meaning into those words alone without context.
You could also ask "can you hear me" on the phone, which would make even less sense face-to-face, unless you're really asking about their hearing or whether you're speaking loud enough.
There are lots of other ways to ask if somebody understands you, but it can depend on why you're even asking. E.g., whether you're asking if somebody understands your English, or whether somebody understands the topic itself.