The other reason a non-profit tries to more than cover its expenses is to accomplish its mission.
The point of non-profits is that their goal is to accomplish something other than profiting. Sometimes the goal can cost a lot of money to accomplish, often much more than just the cost of paying its employees.
For example a non-profit that raises money for cancer research might have very low costs and raise tons of money without raising eyebrows. Because they put the majority toward their goal, and everybody understands the goal, and "profit" is not that goal.
The point of non-profits is that their goal is to accomplish something other than profiting. Sometimes the goal can cost a lot of money to accomplish, often much more than just the cost of paying its employees.
For example a non-profit that raises money for cancer research might have very low costs and raise tons of money without raising eyebrows. Because they put the majority toward their goal, and everybody understands the goal, and "profit" is not that goal.