That's the way Pathfinder works. But not the way Pathfinder Society works. They publish adventures that are only accessible via a PDF file. Yes, the rules and such are available in book format. But we're discussing the adventures, not the rules. It's also the same way that Living Forgotten Realms adventures have been distributed for years, and Living Greyhawk before it.
The only real difference is that LFR, LG, and PFS adventures are free. The D&D Encounters program is run by the Wizards Play division, the same people who run LFR. It was briefly discussed when LFR first came out that charging for adventures even though they were only available via PDF would help by allowing us to pay the writers instead of relying on volunteers. It was rejected however, as WOTC felt that no one would show up to play if they had to pay for adventures, they wanted it to be as accessible as possible. WOTC instead decided to pay adventure authors out of their advertising budget and give the adventures away for free to try to get the best of both worlds.
It looks like the decision making process might have come full circle and now they've decided to charge Encounters DMs in order to get the adventure so they can run them in stores as advertising for WOTC. Not sure how I feel about this. It allows the Encounters adventures to finally be distributed to people who aren't running the adventure in store, which is good. However, it now is a drain on the DMs who really should be rewarded for DMing rather than charged. Maybe they could give a couple free copies of the PDF to each store to give to DMs.