I don't see him sexually assaulting a female in a public bathroom in a college bar. Unless this was a small bathroom with only one toilet, those places might as well have a revolving door making it virtually impossible to have forceable sex. That is just my opinion.
After working college bars for years as security, I can tell you that this happens regularly with people engaging in consentual sex, and more than a few females have been attacked over the years.
Also Ben is a huge star in the NFL and it is ultimately going to come down to a he said/she said debate in the courtroom, and the DA's may not have felt they may not get a conviction based on his status and did not want to waste the resources for a case that would have an iffy outcome at best.
Personally I have no doubt Ben is probably guilty as this type of thing keeps dogging him, and he keeps putting himslef into bad situations with poor choices. Where there is smoke, there usually is fire.