Probably.  But the answer may turn on whether the charity is a public charity or a private foundation. 

Ordinarily, a public charity may enter into an economic transaction with an employee.  This is true even if the employee is a “disqualified person” with respect to the charity, so long as the compensation is reasonable.  With a public charity, a disqualified person includes not only a director or an officer (including the individuals who perform the functions of a chief executive officer, chief operating officer, or chief financial officer) but also any person who has been in a position to exercise substantial influence over the affairs of the organization within the last five years.  (Tax Code Section 4958) As the only employee, the person receiving this rent is likely to be considered a disqualified person with respect to a public charity under one or more of these concepts.

Being a disqualified person for a public charity does not prohibit the rental payment, however, so long as it is reasonable.  If the employee’s home is where the charity’s records are kept and the work of the organization is done, particularly if it is the public address of the organization, it seems unlikely that $100 a month would be considered excessive.  There is a simple way to obtain a rebuttable presumption of reasonableness by following certain “safe-harbor” procedures if the board is concerned. (See Ready Reference Page: “Charities Must Avoid Excess Benefit Transactions”)

If the organization is a private foundation and the person is a disqualified person with respect to the private foundation, however, the rent is a “self-dealing” transaction without regard to whether or not it is fair or reasonable.  It is subject to an excise tax and effectively prohibited.  (See Ready Reference Page: “Private Foundations Must Avoid Self-Dealing”) The definition of disqualified person with respect to a private foundation includes substantial contributors and foundation managers, including directors, officers and those exercising the powers of an officer.  It does not extend generally to individuals in a position to exercise substantial control over the affairs of the organization.  (Tax Code Section 4946) If the employee is strictly an administrative person working as directed by the president or the board, he/she may not be a disqualified person.  But accurately classifying the employee in this case would make the difference in whether the payment is okay or not.