We didn't want to take any of the tour packages for our trip to Isla Mujeres, because they all included so much stuff we weren't interested in. Plus, we always want to save money! We took the bus to the area where the ferries leave. We had to stop at downtown Cancun to change bus lines, but other than that, it was very easy to get there.
Once there, it was $14 round-trip for the ferry boat ride to the island. It was about a 40-minute boat ride, and then we were there! Beware of all the hagglers when you get off the ferry. We strided right past them and walked onto the other side of the shopping area, about three streets down.
We planned on renting a golf cart to tour the island. You could rent scooters, bikes, etc. to help you get around. Our concierge highly recommended renting the golf cart because of the hot sun and the fact that it offers shade. We soon realized that this was a necessity, as there is no shade on the island and it was hot. We rented the golf cart all day for $40 and off we went!
We did a huge loop around the island and then explored the inner portion afterwards. If you go to Cancun, you have to go here. It was the most beautiful adventure for us, especially since we weren't stuck with a group and forced to do things we didn't want to do. We made note when the ferries left the port and just decided to set our own schedule based on that. I would highly recommend doing it this way. We found a beach, parked the cart, and went for a dip. You want to definitely wear your swimsuits so you can do this. We were swimming out where these huge yachts were anchored in. It was amazing. Then we explored the cliffs and went up in the lighthouse. There were so many things to see and explore, I can't even begin. I can't recommend this enough!