Hobart Jr and a few of the other rabbits survive because they blend in to the environment easier. The foxes are still there but they can't catch as many rabbits because the rabbits that have survived blend in better.
The rabbits that are still alive reproduce and a lot of their characteristics are passed on to their offspring. The rabbits are adapting to their environment and increasing their chance of survival.
The darker rabbits were able to blend in with the trees in the forrest. This allowed them to survive longer because the foxes were not able to see them and eat them as easily. This is how the population of rabbits began with Hobart, who was not adapted, changed over time so that Hobart Jr the 2nd's generation was adapted and could survive better.