There is no dearth of transportation options in Johor thanks to Larkin Bus Terminal, which acts as the southern gateway to the Malaysian peninsular. Every major bus company in Malaysia has a counter at Larkin Bus Terminal, and buses from here depart to all major towns and cities across the country.
Taxis are a little trickier. Most taxi drivers in Malaysia do not go by meter, so your haggling skills have to be pretty convincing. Also, not all cabs are legal. Some individuals moonlight as private drivers for extra money, and while this may not seem like a big deal, remember that taxis are covered by insurance while these private cars are not. You can spot a real taxi by its characteristic red-and-yellow look as well as its owner's name and address written on the driver's door.
The state of Johor is also home to Pulau Sibu, and if that is your destination then head down to Tanjung Leman jetty.
A ferry from Mersing Jetty (RM70 return) will get you to the popular tourist destination that is Pulau Tioman. You can also take speedboats from Mersing to Pulau Rawa, Pulau Pemanggil and Pulau Besar.