The Prophet is a Commander who was turned into an Prophet by the command become Prophet. You can normally just have one prophet at a time. If your prophet dies, you must wait some turns before you get a message that you can make a new prophet. The biggest advantate of an prophet is that he spread Dominion like your Pretender. He is also permanently blessed, even if he was not sacred. He also get priest skills of level 3. If he already had 3 or more priest skills, he get priest skill +1.
With priest skill 3, your Prophet can cast such useful spells as smite and divine blessing without any research.
Note: Mictlan in some Eras can spread Dominion only with the Pretender and with Blood Sacrifies.
Note: It is possible by commander-kidnapping to corrupt enemy Prophet's so that you have more acting Prophets who spread your Dominion.