People working on their laptops are actually not a paying customer. Yes, they might come in and buy a single coffee but then they sit in a corner for 3 hours and occupy a seat that could go to other customers that are actually buying things that make a cafe money.
It also has something to do with atmosphere. A cafe should have light chatter and people socializing. If the majority is sitting around in silence, it takes away from the special feeling a cafe normally has. I could get coffee at home for a fraction of the price.