Use fine mesh netting over the hutch's wire cage section, as well as any other areas on the hutch that a snake can slither in. Apply caulk to any cracks and open areas on the wooden section of the hutch, to prevent snakes from entering.
Remove items from your yard that can be used as a "snake habitat," such as piles of sticks, leaves and boards, debris, trash, bricks and stones. Keep vegetation cut back as well. Another benefit of removing such items is it also removes rat and mice habitats, two animals snakes feed on. Snakes are less likely to enter your yard when food and shelter sources are removed.
Create a snake repellent border around your rabbit hutch by sprinkling cinnamon around your hutch's perimeter. Snakes are repulsed by the scent of cinnamon, as well as the smell of clove and cedar oil, and sulfur. Wipe down the hutch with clove and cedar oil, though sulfur should be used as a last resort due to its pungent stench. Use it around your property's perimeter, if desired, rather than around rabbit hutches. Hutches made of cedar wood are another option.