They are used for multiple reasons, for example: after repotting they are strategically placed around the trunk to focus nutrients in certain areas for root growth. You'll see multiple containers used, then in a couple months they'll be rotated around new areas to encourage more roots in other spots.
Another reason is that organic fertilizers can clog up the substrate as it breaks down, so the containers are used to keep the solids in place and only let the broken down particles through into the soil. Also, these particles can become hydrophobic if mixed in with the soil and they'll create dry spots in the soil that will actually repel water until thoroughly saturated.
Keep in mind critters love organic fertilizer (most of the time it's poop, bone meal, blood meal; really stinky stuff...) and they'll steal your bags. Some people will stake these bags into the soil or use wire to secure them in place.