They are called profit shops because both the seller and the buyer can make a profit from the shop.
The players who own the shops and sell items like eggs, iron and cactus make a profit because they are selling items that they can get for free by using their farms. Meanwhile, the players who buy from the profit shops can also make a profit by selling the items for more then they spent on them at the shop.
Basic Example:
You can sell 16x Eggs for $32 by doing /sell h. If an egg profit shop is selling 16x Eggs for $16, you could buy 16x Eggs for $16, then do /sell h (earn $32) and instantly make a $16 profit. The person selling you the eggs also makes a $16 profit from the money you paid to buy the eggs in the first place.