The best way to earn Resistance points is by completing story and Gun-For-Hire missions -- both of those give a lot of RP, but they are not always available. The next best for earning RP are outpost liberations. The map is covered in outposts, and it helps to complete some of the minor RP tasks while you are traveling between outposts, or even while you are in an outpost. If there is a Gun-For-Hire mission available, it is recommended to take it. When you are out of those, you can liberate outposts while destroying silos, smashing shrines, blowing up VIPs/supply vehicles, and saving hostages. All the minor activities are worth doing in conjunction with outposts, but they are not worth tracking down alone. There is no reason to run around and only complete these minor jobs. The following is a list of all Resistance point activities and the RP earned for completing them:

600-900 RP: Story missions
600-900 RP: Gun-For-Hire missions
400 RP: Liberate Outposts
200 RP: Clutch Nixon challenge
100-200 RP: Side missions
100 RP: Destroy Silos
100 RP: Destroy Shrines
75 RP: Destroy Roadblocks
75 RP: Destroy Supply Vehicles
50 RP: Save Hostages
50 RP: Kill Cult VIPs

There are three regions you need to liberate from cult control, and each one is ruled by an evil brother or sister of Joseph Seed, the leader of the cult. As you progress through the region meters, you will reach different levels of resistance. Each time you go up a level, you will be unlock a cutscene, and things will change in the region. More allies and difficult enemies will appear. To unlock the story mission of each region, you must earn the indicated amount of RP:

John's region: 13,000 RP
Jacob's region: 10,000 RP
Faith's region: 13,000 RP

At each level of the resistance, different events will occur in the region (each region has its own special events). Faith will spread drugs throughout her territory, while Jacob hunts and captures more civilians for his cult initiation techniques. The following are the events that occur at the different levels:

Level 1: The resistance is at its weakest. The cult operates openly everywhere.

Level 2: The resistance begins taking back locations and defending them. The cult reacts with special events. Drugging, kidnapping, or blocking roads.

Level 3: The resistance fights back everywhere, and the cult is forced to hide in their enclaves. The regional leader sends airplanes to hunt the player.

That is basically how progression works in the game. To complete the game, you must reach the resistance meter threshold in all three regions, then confront Joseph Seed.