In my experience, there are many good reasons why these cases get pled out:
(1) The burden of proof is extremely high. Proof beyond a reasonable doubt is a tough standard, especially when you typically only have one behind closed doors witness and little corroborating evidence. Things get murkier when there are elements of consent in the statements of the Defendant ("she seemed into it too") as well as the behavior of the victim ("I started kissing him...").
(2) The right to remain silent means the case will be about the victim, her credibility (she's repeated her account so many times there are bound to be inconsistencies), her behavior both before and after, and her culpability (i.e. how she dressed, was she flirty, did she drink too much etc.). While the victim may be cross examined by a hostile defense attorney for hours, the Defendant doesn't have to present evidence and doesn't have to testify.
(3) It's a public process. Aside from having to testify AGAIN (she's already told the cops, the docs, the DA, the grand jury, the DA again in trial prep), she must now do it in front of the Defendant, his family, his lawyer(s), a judge, the media, various court staff and interested persons, and 12 strangers who get to pass judgment on what she says. It's incredibly draining and highly intimidating.
(4) The requirement of a unanimous verdict means that one vote to acquit can result in a mistrial, which means going through the process all over again just because one person wasn't convinced of guilt. Who wants to go through this twice?
(5) If the Defendant has no criminal record, it's going to be difficult to convince a judge to send the guy to prison unless some sort of added forcible element is involved (I understand that it's a crime of violence but without a weapon, evidence of drugging, injuries or the like, this will act as mitigation). Here too, the victim's behavior will be reviewed to determine how "culpable" the Defendant was. In the judge's head, the clean cut kid with the nice suit and slick lawyer is being compared to drug dealers, armed robbers, and wife beaters with many past crimes, and if the victim comes off as a promiscuous and/or troubled woman (as is often the case), that too will play in the Defendant's favor.
Any one of the elements listed above can cause the victim/prosecutor to punt and seek a plea deal. More often than not, it is the victim who caves because of the trauma of it all. The criminal justice system is not designed to handle these types of cases in any sort of humane way. All benefits go towards the Defendant and it is the victim who is effectively put on trial from beginning to end. It takes a really special and courageous person to see it through.