Rape is absolutely forbidden in the US military. So is sexual harassment, in all its forms, and sex discrimination (with some institutional exceptions). The problem, much like other work environments in which women have relatively recently become common, is that mid-level supervisors - senior sergeants in the Army, somewhat equivalent to factory foremen - have (1) careers that predate the arrival of women to the combat environment and (2) a "keep everything within the team" mindset that combine to make this issue very hard for them to deal with. The result is that they tend to actually believe junior sergeants when they say "oh, she consented and then changed her mind afterwards", blow the whole thing off, and never elevate it to officer (management) level.

Training, retraining, and disciplinary actions for those who cannot accept that times have changed is vital. Another problem, of course, is that the military is so stretched and stressed by the stupidity in Iraq that they can barely get mission-essential training (training that is directly related to their military mission) done before they are sent back to the sandbox.