Most hackathons, like the Greylock one mentioned, are organized with large budgets in hopes of bringing in talent to find recruits for their companies.

Independently organized hackathons like AngelHack need to charge to ensure long-term sustainability of the event and ensure you're getting certain amenities that you should expect from a quality hack. If you've ever been to a Facebook hackathon you can tell they spend easily 20k between setup, employees, food costs, travel, and prizes.

If PenApps isn't charging yet, then that's because they are being subsidized by UPenn, which is an awesome luxury that most potential organizers will not have.