This is mainly a matter of opinion. In my opinion, this concentration is generally justified.
It makes sense that the correctional system would be focused on the population that is both larger and more dangerous to the public. Therefore, it makes sense that the correctional system should focus on men. The vast majority of women who are incarcerated are there for nonviolent crimes. Therefore, it stands to reason that the prison system should be less concerned with them than with the men, many more of whom are in for violent crimes.
A major role of the prison system is to protect the public. A concentration on men more than women is likely to do more to protect the public than a concentration on women would be.