Working for a Good Cause has its Benefits. Working in a nonprofit organization brings both material and nonmaterial rewards. Although some nonprofit organizations do not pay (or are unable to pay) market wages, the benefits of working in a nonprofit often outweigh the drawbacks for many employees. The pay structure at a nonprofit organization, like that of a for-profit company, begins with the compensation of the top executive. 2  If he or she is paid less than market, it will disrupt the internal equity of the organization and everyone will reach a pay ceiling.