Quite. It's not use that patents are supposed to prevent, it's imitation. If you invent the autofoo, patenting it gives you certain rights to benefit materially from that invention (I'm sure you expect some reward for your effort, and quite right too); this includes control of the manufacture of autofoos (if someone wants to manufacture autofoos, they need to get your permission and presumably pay you a licensing fee). What happens to those autofoos once they've left the market and gone into the street is not up to you, but you can crack down on any rival autofoo manufacturers who are out there stealing food from the mouths of your children.
Same with patenting the concept of an online shopping cart, or downloadable video, paying by credit card over the Internet, or thumbnail images (just to pick three examples of patented concepts). If you've patented one of those, then you've got legal prevention against anyone else building the same thing for their site or distribution. Because every time someone comes up with the idea of putting a thumbnail on their site (since that is what was patented - not the implementation, but the concept), then that's an infringment on your patent rights (assuming that you're the person who patented the thumbnail image: I'm guessing you're not🙂).
Of course, if you don't have a product, then they're legally screwed - they can't use yours and they can't make their own. But that's their problem, not yours, right?
Incidentally, I'm reminded of the occasional myths along the lines that someone invents a car engine that runs on water, but the oil barons bought the patent for squillions of dollars so that no-one would be able to manufacture it (and they're certainly not about to start). Problem with the story, of course, is that patents are necessarily a matter of public record.
All in all, Rodney H.'s point (1) is the strongest defence (I'm arguing with myself about whether the contract should mention the gist of point (2)....).
And if, ultimately, your software becomes widely pirated despite points (1), (2), and (3), then at least it's your software that's being pirated, and with luck rogue users will become so hitched to it that when they do want to go legit there's only one supplier (which is why Microsoft isn't too upset about the number of illicit copies of Windows floating around in China.)
