I have not been to the mainland, mainly because I do not want to deal with long transfers from the airpot to destination. I prefer Cozumel, you can get a direct flight righ on the island. The island is very safe. Love love love it. The island is considered to be one of the safest places to travel. Petty theft is abotu the only concern, but that is anywhere their is tourist. even here.
But if you do go to the mainland, most of you hotels should provide a shuttle from the airport, just make sure you follow thier directions on making sure you get on the right shuttle service you will be fine.