In terms of technology, there is no difference at all between the green, red and amber fobs.
Companies use the different colours to provide a visual means of demarcating access to different areas of the building.
For example, green fobs may be given to users who only have access to Area A, whereas amber fobs could be given to users who have access to Areas A & B. Red fobs could be given to users who have access to Areas A and C, and so on.
In other words, you can use the colour coded fob system to control different user rights.