If I have a patent on X, that means I can charge you money to make X.

Suppose X is sandwiches. If I'm allowed to charge anyone who makes sandwiches, yes, my patent is worth lots of money. It's not "worthless" in that sense. It's worthless in the societal sense: allowing my monopoly provides no value to society.

Nobody thinks you can't make money from software patents. Some people think software patents do not provide value to society by encouraging innovation, which is the stated legal intention of intellectual property law.