I don't recommend using soap unless you're sure you can get all the soap off the pacifier.
Come to think about it putting some soap on the pacifier would be a good way to get a toddler to give up their pacifier.
A good way to keep pacifier clean is by rinsing it in hot water or dipping it in some boiling water using some tongs.
Don't leave the pacifier in the boiling water for too long though as you might melt the silicone pacifier nipple.
Just dip the pacifier in the boiling water for a few seconds at a time and swish it around and the boiling water will kill the germs.