It is normal for a charger to get a little warm and maybe a bit hot from time to time as it's working. Sometimes there may even be an odor. It really depends on the battery charger and how long it's been running and how hard it has to work. The charger may get hot from time to time depending on how far the batteries were discharged and how long it takes to bring the batteries back up to 100% charged. But here are a few general tips to keep the charger from overheating: 

Make sure that your battery cable connections are correct, clean and tight. Bad connections can cause a charger to overwork and overheat. 

Ensure that you have adequate water levels in your batteries. 

Do not use an extension cord. If you must use one, just use a heavy-duty extension cord. A cheap extension cord can cause the charger to overheat. 

Give the charger room to breathe and make sure it is on a hard surface, preferably the garage floor. 

With that said, if the golf cart charger is always hot and always giving off a bad smell, you should contact the manufacturer to confirm that everything is functioning properly.