Install shutters outside all your windows. For the best results, you should be able to close them from inside. Shut and lock your shutters before storms to protect your windows. This is a good step to take to prevent break-ins when you're away on vacation, also.
Buy and install protective glass film on the exterior of your windows. This durable, thin and clear plastic film can prevent flying objects, rain and wind from cracking or shattering your glass windows.
Place plywood sheets outside your windows and hold them in place with window clips. Window clips protect the glass from heavy rain and airborne debris without the need for nails or screws.