They are being employed by the NCR force as a mean to find more NCR citizens in the area, so they can provide them with food and water. Each missionary is located in the squatter camps you are originally sent to investigate, they are the quest markers.
G.I. Blues: The King gives the player the optional objective to investigate the NCR squatters in Freeside to find out more about the people who attacked his men. The player can ignore that and go directly to Julie Farkas who will send you to talk to her friend, Major Elizabeth Kieran who is in charge of the food supplies at the Ruined store.
Either will ask the player if they are a citizen of the NCR. If the player answers "yes", the player is quizzed with three questions to prove that they are an NCR Citizen.
Question 1 - Who is the most popular NCR President of all time? President Tandi.
This will give you access to Missionary's note, which reads cryptically "Hope is the key." Hope is actually the password you give to the two NCR guards outside the ruined store they use to supply the NCR Freeside members with food and water. This note can also be obtained by killing the missionaries.