It's a huge problem, because lying about rape does happen but it's very rare. Women need to be taken seriously in these accusations, but the risk carried with falsely accusing someone can stick to them forever, even if it's just in the court of public opinion. The Duke University scandal is a great lesson on this, and a lot of people still remember that case as them being guilty, even though they were very much not guilty.
Being falsely accused of rape is something that no man will ever escape. Rape is such an awful crime and there is a conventional wisdom that it is under reported so the falsely accused will likely never escape the charge in some people's eyes. It's unfortunate, but is the truth.
A person accused of a crime, especially one as heinous as rape, has a very difficult time overcoming the allegations, even after being proven false. Without an abundance of evidence or confession from the accuser, many people will still believe that the person is guilty, whether or not the person has been cleared by the law.
No, a male student falsely accused of rape can never be free from the repercussions of the accusation. As far as sexual assault is concerned, we live in a culture where the accused is assumed to be guilty until proven innocent. This makes it possible for false accusations to ruin lives.