I went on a really cool trip with Alltournative to the Sian Ka'an biosphere yesterday (more on that in Things to do, coming up).
I was shocked to find out how much some of the AI's mark up the prices of local tours. You can buy a trip to Chichen Itza for around 40usd in town. At Bahia Principe, they charge 95! (same tour, same company)
Same goes for AI's in Playacar, but I think they charge about 70usd for the 40usd trip.
I was told by several AI guests that they are invited to a welcoming meeting where they are warned about venturing out on their own, renting cars, and the dangers of Playa del Carmen. This has to be part of a scheme to keep everyone buying in-house. The cheap upfront package deals are the hook to charge you unfairly once they get you here.
Of course, maybe not all AI's do this, but please be careful and shop wisely if you choose to go AI.