Witty, I'm hoping your remarks are borne of simply never having been in that situation/talked to a friend who has been in that situation. If you look at the testimony of rape victims (and this is well explained in the psychological literature) it's a gross over-simplification to talk about the "fight or flight" reflex: it is better described as "flight, fight or freeze". It is incredibly common for rape victims simply to freeze and lie there completely inert.
Also, if you read through the #whyIdidn'treport thread (and please, please do not post your ideas about women just needing to say "no" more clearly because men aren't mind readers) you will see that a recurring theme is saying no, or saying "I'm okay with X but not Y" and having that ignored.
There's a very good chapter in Deborah Cameron's book "The Myth of Mars and Venus" on the whole idea that "men are just rubbish communicators" which debunks that idea. Both sexes are able to read subtle signs and body language - rapists choose to pretend that they can't.
Also, you might find the work of American criminal psychologist David Lisak interesting. When he carries out surveys of randomly selected college students and asks them about behaviour patterns without mentioning the word rape, behaviours like "have you ever had sex with a woman when you knew she didn't want it, by using your body weight to restrain her?", 6% of men admit to behaviours which meet the legal definition of rape. When he repeats those questionnaires explicitly asking "have you ever raped a woman?" the percentage drops to 5%.
This strongly suggests that most rapists know exactly what they are doing. They don't care. They know that if they already know the woman, or have been seen drinking with her in a bar, or she's drunk, the chances of them being convicted are next to zero.
That is why we don't need advice like "make sure he understands 'no'". Chances are he understands damn fine. It's not rocket science. What we need is a sea change in public attitude, and a change in the way rape is prosecuted. So that it become routine for prosecution lawyers to ask "What exactly made you think this woman wanted sex at this particular time in these particular circumstances?" And where when it's her word ("I lay there motionless and crying") against his ("She loved it") juries are more prepared to believe the woman's testimony.