If transferring from CUN to the ferry I’d look at one of the preferred transfers like Canada or USA Transfers just for convenience and peace of mind. There are also less expensive shared vans outside terminal 3, and I don’t know if an ADO bus makes that route but you could check.
Actually the first thread in the Top Questions on the TA Isla Mujeres forum provides excellent info on your transfer question.
https://www.tripadvisor.com/ShowForum-g150810-i360-Isla_Mujeres_Yucatan_Peninsula.html