My sense is that sexual assaults are still far less prevalent at service academies than on the campuses of civilian colleges. As Luigi and other posters have correctly noted, most sexual assaults on college campuses fall into the "acquaintance category" ("acquaintance rape" is often a more accurate term than "date rape" given the norms of college-age socializing these days), and are overwhelmingly correlated with alcohol use.
Even with the access to alcohol that exists in today's service academies, there is still far less drinking on campus grounds than at your typical residentially-oriented college/university. For one thing, you can't go on a bender and miss a day or two of classes; for another, there is more adult supervision.
Why, then, does it seem like there are frequent articles about sexual assaults at SAs? Some of this is the nature of reporting. Harvard's statistics are in the aggregate (as are those of all the civilian colleges); because of the nature of the military justice system, the names of the accused are made public. Only if "outside" law enforcement officially charges a civilian college student will the name be made public, and acquaintance rape cases are so difficult to prove under criminal standards that many victims choose a non-judicial avenue of redress (e.g., reporting within their college's disciplinary system, which could result in the alleged wrongdoer being barred from campus, or suspended, or asked to withdraw, based on a lower standard of proof than the very high "reasonable doubt" criminal standard. (Google the case of Yale's recent NOT Rhodes Scholar candidate QB for a window into the non-judicial avenues for pursuing a campus sexual assault case.)
Second, as Luigi says, I do believe the public holds SA students to a higher standard (which, by the way, most of them meet and then some, in my experience). People do sometimes forget that with a sample size of 1000-4000 young people drawn from every part of the country and every background, larger social issues of concern for that age group will pop up in the Brigade/Corps/Wing. If 18 year olds drink, there will be cadets/mids who do so. Addicted to video games? Using adderol to study? Smoking pot? Ditto, ditto, and ditto. Even though the bad behavior is at a much lower rate (I assume and believe) than your typical college population, it still surprises and disappoints the public to hear of it.
For my own daughters, one of whom has expressed interest in pursuing a commission, risk of sexual assault should she attend a service academy is truly the last thing I worry about. (We have talked and will keep talking about safe behavior in social situations involving alcohol, as that issue will arise anywhere.) I do think there are some cultural implications to an 80-20% male/female breakdown, and I will want her to think about whether that environment is for her (pluses and minuses compared to ROTC), but her physical safety is not an issue for a nanosecond.