Is it illegal for someone to charge their roommate rent that, together, equals the total amount of rent owed and them not pay anything?

Parties may enter into any agreement that they want as long as it does not violate public policy or state statute.  The contract that you are referring to is a smple lease agreement.  parties to a lease may contract for rent at any price they mutually agree to.  In this case, the sole tenat on the lease has sublet 2 rooms to 2 different people and charging rent based on what the 2 paries agreed to as fair rent for the room.  it does not matter what the tenant is paying on the lease that determines how much you are subletting the room for.  rather, the tenat on the lease is simply making a smart business decision where he rented an apartment and rented out the rooms so he could live there for free.  there is nothing illegal about this.