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 gets a priest skill of level 3. If he already had 3 or more priest levels, he receives a +1 bonus to his priest level.
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.