The charity shops raise funds for whichever charity oversees them. I used to work in a hospice and it depended very much on the income from sales in the charity shops to raise money to keep it going. Same as PDSA, barnardos, whatever, the money raised goes back into the charity.
The shops usually paid reduced rent and rates because they are registered charities and they often have a paid manager, but you are right, the rest of the staff are usually volunteers.