They take the money from what they collect. That's why for evey pound you give to charity, on average , only 14p actually makes it to the good cause. The rest is swallowed up by employeesand running costs within the charity. Think about this. How much do you think the RSPCA pay, firstly to make a 30 second TV commercial and then to air the commercial on terestrial and satalite tv channels? It aint cheap!
Better to think of this Sector as 'not for profit'. The vast majority of the people that work for them are paid the same as anywhere else. A small number, particularly in 'not for profit' shops may be volunteer workers. Any founder or the directors still take a salary. The real difference is that there are no shareholders or owners to pay a divident to.