Having played a cyberpunk version of the GURPS roleplaying game, as well as a few sessions of Shadowrun back in the 90's, I'm not having as hard a time as I might in following Gibson's Neuromancer. That being said, I'm surprised that anyone who has seen The Matrix movies would have difficulty following the story at the halfway point.
The single most confusing aspect of the novel should be all the new terminology being thrown around, and I think most of it makes sense. There are certainly terms that I don't know, with the heavy use of Japanese throughout the story. But who among us can't figure out what Gibson is referring to when Case is "jacked in"...picture a hole in the back of Neo's head...and while everyone isn't immersed into this matrix, you quickly visualize what's going on. Even the description that Gibson gives in Case's early internal monologue monologue (“bright lattices of logic unfolding across that colorless void”) takes us straight to the matrix as it appears on the screens in the Nebuchadnezzar.
For the most part, Neuromancer is a mystery unfolding around the character of Case. It just happens to be set in the realm of Science Fiction. Any confusion from the circumstances themselves, should be there, I think.