That is almost like saying a car should cost less because someone else drives a car 5,000 miles a year when I drive mine 40,000. It's the same amount of labor and materials to build that car, no matter how it is used.
And no, big boards should not pay more, not for the same software. However, if XF provided a version with numerous performance and feature enhancements for big boards, we would gladly pay it. But see, we'd be paying for that enhanced software, and the extra money they'd take in would cover the expense in programming labor it took to create it.
One smaller forum of mine gladly chipped in to upgrade us away from "free forum software hell". And quite frankly it was a relief, as I was sick of constantly having to patch the forum, modify it, etc. to keep the hackers and spammers out, and add features that "real" packages had, like vB (at the time) and others. Not to mention the lack of version upgrades, and the lack of support (other than a snotty support forum). You do get what you pay for here, and the safety net of having support, with developers who actually stay in contact with their customers, is something we value more than the money we parted with. Granted, XF isn't 100% perfect for our needs either, but with some supported add-ons, and a staff that at least listens to our suggestions, I don't think we could have found a better package overall.